Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_069665193.1 BCR25_RS19025 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_001730305.1:WP_069665193.1 Length = 341 Score = 355 bits (911), Expect = e-103 Identities = 172/333 (51%), Positives = 241/333 (72%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60 MIV++K +T+ I+ V++ + L+ H+S+G+E+T+IG++GD R + F S D VE Sbjct: 1 MIVIMKSEATKAQIKSVIERVKKEGLEVHLSEGKEQTIIGLVGDTRKMQDVAFNSYDGVE 60 Query: 61 SVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSEL 120 + VR+ YKL SREFHPE+T++D+ VKIG+G T++AGPCS+EG + + E A Sbjct: 61 NAVRISLTYKLTSREFHPENTIVDVDGVKIGDGSMTMMAGPCSIEGLDQIRECARIAKAG 120 Query: 121 GVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADI 180 G +LRGGA+KPRTSPY+FQGL E+GL+Y+R+AAD++ M V+TE + E + +AEY+DI Sbjct: 121 GATILRGGAFKPRTSPYAFQGLEEEGLKYIRQAADEFDMKVITEVMDEGHIDMIAEYSDI 180 Query: 181 IQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIR 240 +QIGARN QNF+LL G KP+ LKRG TI+E+L +AEYIA GN +I ERGIR Sbjct: 181 LQIGARNMQNFKLLQAVGKTGKPIGLKRGISGTIDEWLNAAEYIAAQGNFNVIFIERGIR 240 Query: 241 TFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVH 300 T+E ATRNTLD+SAVP+I+K SH PI+VDPSH G DLV ++RA +A GA G+IVE+H Sbjct: 241 TYETATRNTLDLSAVPLIKKLSHFPIIVDPSHGVGIWDLVPSMARAGVAAGADGLIVEIH 300 Query: 301 PEPEKALSDGKQSLDFELFKELVQEMKKLADAL 333 P+P A SDG QSL+ + + ++QE+ + A+ Sbjct: 301 PDPVNAWSDGPQSLNEKTYMRMMQEVHIMEKAM 333 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: 327 Number of extensions: 7 Number of successful extensions: 1 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: 341 Length adjustment: 28 Effective length of query: 310 Effective length of database: 313 Effective search space: 97030 Effective search space used: 97030 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_069665193.1 BCR25_RS19025 (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.2215536.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-129 415.2 0.0 6.6e-129 414.8 0.0 1.2 1 NCBI__GCF_001730305.1:WP_069665193.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001730305.1:WP_069665193.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 414.8 0.0 6.6e-129 6.6e-129 2 259 .. 71 328 .. 70 329 .. 0.99 Alignments for each domain: == domain 1 score: 414.8 bits; conditional E-value: 6.6e-129 TIGR01361 2 laskkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysfqGlg 74 l+s+++++e+t+vdv++vkiG+g+++++aGPCs+e +qi+e+a+ k+ Ga++lrGgafkPrtsPy+fqGl+ NCBI__GCF_001730305.1:WP_069665193.1 71 LTSREFHPENTIVDVDGVKIGDGSMTMMAGPCSIEGLDQIRECARIAKAGGATILRGGAFKPRTSPYAFQGLE 143 78*********************************************************************** PP TIGR01361 75 eeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkrglaatiee 147 eeglk++++a+de++++v+tev+de +++++aey DilqiGarnmqnf+lL++vgk+ kP+ Lkrg++ ti+e NCBI__GCF_001730305.1:WP_069665193.1 144 EEGLKYIRQAADEFDMKVITEVMDEGHIDMIAEYSDILQIGARNMQNFKLLQAVGKTGKPIGLKRGISGTIDE 216 ************************************************************************* PP TIGR01361 148 wleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrrdlvlplakaava 220 wl+aaeYi+++gn nvi++erGirt+e+atr+tldlsav+l+kkl+h+P+ivDpsh++G +dlv+++a+a+va NCBI__GCF_001730305.1:WP_069665193.1 217 WLNAAEYIAAQGNFNVIFIERGIRTYETATRNTLDLSAVPLIKKLSHFPIIVDPSHGVGIWDLVPSMARAGVA 289 ************************************************************************* PP TIGR01361 221 vGadgllievhpdPekalsDseqqltpeefkelvkelka 259 +Gadgl++e+hpdP +a+sD++q+l+++++ ++++e+++ NCBI__GCF_001730305.1:WP_069665193.1 290 AGADGLIVEIHPDPVNAWSDGPQSLNEKTYMRMMQEVHI 328 ************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (341 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: 00:00:00.00 # Mc/sec: 19.36 // [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