Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_012283048.1 HM1_RS08950 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000019165.1:WP_012283048.1 Length = 337 Score = 330 bits (846), Expect = 3e-95 Identities = 168/333 (50%), Positives = 231/333 (69%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60 M++V+ P +T+ I KV ++ Y H+ G R VIG +GD + + + E+L VE Sbjct: 1 MVIVMTPNATQTQIEKVNQILAEYGFAGHMITGVNRIVIGAVGDRQAIASLGLETLAGVE 60 Query: 61 SVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSEL 120 VV + +PYKLVSRE E+T++ + DV IG T+I GPC++E E +M A + Sbjct: 61 KVVPIRRPYKLVSREAKEENTIVHVKDVAIGGDAVTVIGGPCAIESVEQVMRAAEEVRRC 120 Query: 121 GVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADI 180 G K+LRGGA+KPRTSPY+FQGL E GL+ LR A G+ V+E + E L ++Y D+ Sbjct: 121 GGKILRGGAFKPRTSPYAFQGLEEDGLKILRIAGRFAGLPTVSEVIDEASLELASQYLDM 180 Query: 181 IQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIR 240 +QIGARN QNFRLL G PV+LKRG TIEE+L++AEYI + GN+++ILCERGIR Sbjct: 181 VQIGARNMQNFRLLQAVGRARIPVILKRGLSATIEEWLMAAEYILSEGNSQVILCERGIR 240 Query: 241 TFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVH 300 T+E ATRNTLD+SA+P++++ SHLPILVDPSH+ G LV +S+AA+A GA G++VEVH Sbjct: 241 TYETATRNTLDLSAIPLVKELSHLPILVDPSHATGASRLVKSMSKAAVAAGADGLLVEVH 300 Query: 301 PEPEKALSDGKQSLDFELFKELVQEMKKLADAL 333 PEP +AL DG QSLD E F+ L++E+ +A A+ Sbjct: 301 PEPCRALCDGPQSLDPEGFEVLMKELAPVARAV 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: 284 Number of extensions: 10 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: 337 Length adjustment: 28 Effective length of query: 310 Effective length of database: 309 Effective search space: 95790 Effective search space used: 95790 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_012283048.1 HM1_RS08950 (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.25027.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.1e-123 394.7 0.0 1.1e-122 394.4 0.0 1.1 1 lcl|NCBI__GCF_000019165.1:WP_012283048.1 HM1_RS08950 3-deoxy-7-phosphohep Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019165.1:WP_012283048.1 HM1_RS08950 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 394.4 0.0 1.1e-122 1.1e-122 2 257 .. 71 326 .. 70 329 .. 0.99 Alignments for each domain: == domain 1 score: 394.4 bits; conditional E-value: 1.1e-122 TIGR01361 2 laskkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysf 70 l+s++ k+e+t+v+v+dv+iG++ ++vi GPC++es eq++++a++v++ G k+lrGgafkPrtsPy+f lcl|NCBI__GCF_000019165.1:WP_012283048.1 71 LVSREAKEENTIVHVKDVAIGGDAVTVIGGPCAIESVEQVMRAAEEVRRCGGKILRGGAFKPRTSPYAF 139 789****************************************************************** PP TIGR01361 71 qGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkr 139 qGl+e+glk+l+ a +gl++v+ev+de+ +e++++y D++qiGarnmqnf+lL++vg+++ Pv+Lkr lcl|NCBI__GCF_000019165.1:WP_012283048.1 140 QGLEEDGLKILRIAGRFAGLPTVSEVIDEASLELASQYLDMVQIGARNMQNFRLLQAVGRARIPVILKR 208 ********************************************************************* PP TIGR01361 140 glaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrr 208 gl+atieewl+aaeYilsegn++vilcerGirt+e+atr+tldlsa++l+k+l+hlP++vDpsha+G + lcl|NCBI__GCF_000019165.1:WP_012283048.1 209 GLSATIEEWLMAAEYILSEGNSQVILCERGIRTYETATRNTLDLSAIPLVKELSHLPILVDPSHATGAS 277 ********************************************************************* PP TIGR01361 209 dlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkel 257 lv++++kaava+Gadgll+evhp+P +al+D++q+l+pe f+ l+kel lcl|NCBI__GCF_000019165.1:WP_012283048.1 278 RLVKSMSKAAVAAGADGLLVEVHPEPCRALCDGPQSLDPEGFEVLMKEL 326 ***********************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (337 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: 8.89 // [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