Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_004513790.1 GMET_RS00120 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000012925.1:WP_004513790.1 Length = 344 Score = 349 bits (896), Expect = e-101 Identities = 172/336 (51%), Positives = 237/336 (70%), Gaps = 1/336 (0%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60 M++V+ + + I VVK E+ L G ERT IG++G+ YV L V+ Sbjct: 1 MLIVMIHKAGPKQIEAVVKAVETMGLTAAPIPGSERTAIGVLGNKGYVDDTTIRDLPGVQ 60 Query: 61 SVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYF-TIIAGPCSVEGREMLMETAHFLSE 119 V+ V KPYKLVSR+FHP +T++ + + IG G ++AGPC+VEG E +++TA + + Sbjct: 61 EVIHVSKPYKLVSRDFHPRNTIVKVCGISIGEGKRPVVVAGPCAVEGEEQILKTARAVKK 120 Query: 120 LGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYAD 179 G +LRGGA+KPRT P++FQG+ E+GL+ L +A + G+ +VTE + D + VAEYAD Sbjct: 121 AGADLLRGGAFKPRTGPHTFQGMREEGLKLLAKAREATGLPIVTEVMSPDTVGLVAEYAD 180 Query: 180 IIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGI 239 ++Q+GARN QNF LL + G KPVLLKRG TIEEFL +AEYI GN +ILCERGI Sbjct: 181 LLQVGARNMQNFELLKELGRIQKPVLLKRGMSATIEEFLAAAEYILAEGNPHVILCERGI 240 Query: 240 RTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEV 299 RTFE ATRNTLD++ VP+IR+ SHLP++VDPSH+ G+R LV P+++AA+ GAHG+++EV Sbjct: 241 RTFETATRNTLDLAVVPLIREMSHLPVMVDPSHATGKRSLVAPMAKAALVAGAHGVLIEV 300 Query: 300 HPEPEKALSDGKQSLDFELFKELVQEMKKLADALGV 335 HPEP+KALSDG QSL F F L++E+++L LGV Sbjct: 301 HPEPDKALSDGPQSLTFHGFDLLMEEIRRLNAFLGV 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: 10 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: 344 Length adjustment: 29 Effective length of query: 309 Effective length of database: 315 Effective search space: 97335 Effective search space used: 97335 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_004513790.1 GMET_RS00120 (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.20591.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-127 409.4 0.0 3.6e-127 409.1 0.0 1.1 1 lcl|NCBI__GCF_000012925.1:WP_004513790.1 GMET_RS00120 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012925.1:WP_004513790.1 GMET_RS00120 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 409.1 0.0 3.6e-127 3.6e-127 2 258 .. 71 328 .. 70 330 .. 0.99 Alignments for each domain: == domain 1 score: 409.1 bits; conditional E-value: 3.6e-127 TIGR01361 2 laskkvkkeetvvdvedvkiGege.liviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPys 69 l+s+++++++t+v+v +++iGeg+ ++v+aGPC+ve eeqi++ta+avk+aGa+llrGgafkPrt P++ lcl|NCBI__GCF_000012925.1:WP_004513790.1 71 LVSRDFHPRNTIVKVCGISIGEGKrPVVVAGPCAVEGEEQILKTARAVKKAGADLLRGGAFKPRTGPHT 139 789********************989******************************************* PP TIGR01361 70 fqGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLk 138 fqG+ eeglkll++a+++tgl++vtev+ ++ v +vaey+D+lq+GarnmqnfelLke+g+ +kPvlLk lcl|NCBI__GCF_000012925.1:WP_004513790.1 140 FQGMREEGLKLLAKAREATGLPIVTEVMSPDTVGLVAEYADLLQVGARNMQNFELLKELGRIQKPVLLK 208 ********************************************************************* PP TIGR01361 139 rglaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGr 207 rg++atiee+l+aaeYil+egn++vilcerGirtfe+atr+tldl++v+l+++++hlPv+vDpsha+G+ lcl|NCBI__GCF_000012925.1:WP_004513790.1 209 RGMSATIEEFLAAAEYILAEGNPHVILCERGIRTFETATRNTLDLAVVPLIREMSHLPVMVDPSHATGK 277 ********************************************************************* PP TIGR01361 208 rdlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelk 258 r+lv p+akaa+ +Ga+g+lievhp+P+kalsD++q+lt++ f+ l++e++ lcl|NCBI__GCF_000012925.1:WP_004513790.1 278 RSLVAPMAKAALVAGAHGVLIEVHPEPDKALSDGPQSLTFHGFDLLMEEIR 328 ************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (344 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: 13.12 // [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