Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_084056100.1 B9A12_RS02870 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_900176285.1:WP_084056100.1 Length = 357 Score = 367 bits (943), Expect = e-106 Identities = 184/335 (54%), Positives = 249/335 (74%), Gaps = 1/335 (0%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60 MIVV+KP T+E++R ++ E L+ H+SKG+ RT+IG+IGD + F S VE Sbjct: 1 MIVVMKPDHTQEELRDLLARIEKMGLRTHVSKGERRTIIGVIGDRALIQEVPFTSFSGVE 60 Query: 61 SVVRVLKPYKLVSREFHPEDTVIDLGD-VKIGNGYFTIIAGPCSVEGREMLMETAHFLSE 119 + +L+PYKLVSREF EDTV+ +GD V++G IIAGPC+VEGRE+L E A L Sbjct: 61 AAHPILQPYKLVSREFKEEDTVVRIGDHVELGGKAIPIIAGPCAVEGREVLDEIADALHG 120 Query: 120 LGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYAD 179 LGV +LRGGA+KPRTSPYSFQGLGE L+Y+ + ++ GM +VTE + DL V +YAD Sbjct: 121 LGVPMLRGGAFKPRTSPYSFQGLGELALKYMSDVRERTGMPIVTEVMDPRDLLLVHKYAD 180 Query: 180 IIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGI 239 ++QIG RN QNFRLL++ G +KPV+LKRG TI+EFL+SAEYI + GN K+ILCERGI Sbjct: 181 VLQIGTRNMQNFRLLTEVGQVDKPVILKRGMSATIKEFLMSAEYIVSHGNEKVILCERGI 240 Query: 240 RTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEV 299 RTFE TRNTLD+SAVP+++K +HLP++VDPSH+ GR DL+ +S AA+A GA G+++EV Sbjct: 241 RTFESETRNTLDLSAVPLLKKLTHLPVIVDPSHALGRTDLIPAMSCAAVAAGADGLMLEV 300 Query: 300 HPEPEKALSDGKQSLDFELFKELVQEMKKLADALG 334 H P++ALSDG QSL + +L+Q+++ +A A+G Sbjct: 301 HVRPQEALSDGAQSLTPQAMADLLQKLEPVARAVG 335 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: 356 Number of extensions: 8 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: 357 Length adjustment: 29 Effective length of query: 309 Effective length of database: 328 Effective search space: 101352 Effective search space used: 101352 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_084056100.1 B9A12_RS02870 (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.22432.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-119 384.4 0.0 1.6e-119 384.1 0.0 1.1 1 lcl|NCBI__GCF_900176285.1:WP_084056100.1 B9A12_RS02870 3-deoxy-7-phosphoh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176285.1:WP_084056100.1 B9A12_RS02870 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 384.1 0.0 1.6e-119 1.6e-119 2 257 .. 71 327 .. 70 330 .. 0.98 Alignments for each domain: == domain 1 score: 384.1 bits; conditional E-value: 1.6e-119 TIGR01361 2 laskkvkkeetvvdved.vkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPys 69 l+s+++k+e+tvv++ d v++G++ + +iaGPC+ve +e + e+a a++ G+ +lrGgafkPrtsPys lcl|NCBI__GCF_900176285.1:WP_084056100.1 71 LVSREFKEEDTVVRIGDhVELGGKAIPIIAGPCAVEGREVLDEIADALHGLGVPMLRGGAFKPRTSPYS 139 79************98769************************************************** PP TIGR01361 70 fqGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLk 138 fqGlge +lk+++ ++++tg+++vtev+d+rd+ +v++y+D+lqiG+rnmqnf+lL evg+ +kPv+Lk lcl|NCBI__GCF_900176285.1:WP_084056100.1 140 FQGLGELALKYMSDVRERTGMPIVTEVMDPRDLLLVHKYADVLQIGTRNMQNFRLLTEVGQVDKPVILK 208 ********************************************************************* PP TIGR01361 139 rglaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGr 207 rg++ati+e+l++aeYi+s+gne+vilcerGirtfe+ tr+tldlsav+llkklthlPvivDpsha Gr lcl|NCBI__GCF_900176285.1:WP_084056100.1 209 RGMSATIKEFLMSAEYIVSHGNEKVILCERGIRTFESETRNTLDLSAVPLLKKLTHLPVIVDPSHALGR 277 ********************************************************************* PP TIGR01361 208 rdlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkel 257 dl+++++ aava+Gadgl++evh P++alsD++q+ltp+ ++ l+++l lcl|NCBI__GCF_900176285.1:WP_084056100.1 278 TDLIPAMSCAAVAAGADGLMLEVHVRPQEALSDGAQSLTPQAMADLLQKL 327 ********************************************999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (357 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.98 // [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