Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_013842920.1 DESRU_RS14960 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000215085.1:WP_013842920.1 Length = 340 Score = 338 bits (868), Expect = 9e-98 Identities = 171/337 (50%), Positives = 232/337 (68%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60 MI+V+ P + E V++ + + H+S+G ERT+IG I D + ++ VE Sbjct: 1 MIIVMSPKADENKTDAVLERLKRAGFQIHLSQGVERTIIGAIRDRTRMGDLALAAMPGVE 60 Query: 61 SVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSEL 120 SVV +L+PYKL SR F E T++ +GD+ IG ++AGPC+VE RE L+E A + E Sbjct: 61 SVVPILQPYKLASRAFKEEGTIVRVGDIAIGGEEIHVMAGPCAVESREQLLEAARLVKEA 120 Query: 121 GVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADI 180 G +LRGGA+KPRTSPYSFQGL E+GL+ L EA +K G+ VVTE + LP +AEYADI Sbjct: 121 GATLLRGGAFKPRTSPYSFQGLEEEGLKLLAEAREKTGLKVVTEVMDASTLPMIAEYADI 180 Query: 181 IQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIR 240 +QIG RN QNF LL + +KPVLLKRG TIEE+L++AEYI GN +ILCERGIR Sbjct: 181 LQIGTRNMQNFFLLREVAKVDKPVLLKRGVSATIEEWLMAAEYIMAGGNYNVILCERGIR 240 Query: 241 TFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVH 300 T+E TRNTLD++A+P+++ SHLPI+VDPSH+ G+ V P++ AA+A GA G+++EVH Sbjct: 241 TYESFTRNTLDLAAIPVVKHLSHLPIIVDPSHAIGKWRFVPPMAAAAVAAGADGLLIEVH 300 Query: 301 PEPEKALSDGKQSLDFELFKELVQEMKKLADALGVKV 337 P P +AL DG QSL F+ L+Q++K +A G KV Sbjct: 301 PNPAEALCDGPQSLTPTNFQSLMQDLKSVAGVFGRKV 337 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: 315 Number of extensions: 9 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: 340 Length adjustment: 28 Effective length of query: 310 Effective length of database: 312 Effective search space: 96720 Effective search space used: 96720 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_013842920.1 DESRU_RS14960 (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.16697.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-128 412.7 0.0 3.5e-128 412.4 0.0 1.1 1 lcl|NCBI__GCF_000215085.1:WP_013842920.1 DESRU_RS14960 3-deoxy-7-phosphoh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000215085.1:WP_013842920.1 DESRU_RS14960 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.4 0.0 3.5e-128 3.5e-128 2 259 .. 71 328 .. 70 329 .. 0.99 Alignments for each domain: == domain 1 score: 412.4 bits; conditional E-value: 3.5e-128 TIGR01361 2 laskkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysf 70 las+ +k+e t+v+v d++iG++e+ v+aGPC+ves+eq++e+a+ vkeaGa+llrGgafkPrtsPysf lcl|NCBI__GCF_000215085.1:WP_013842920.1 71 LASRAFKEEGTIVRVGDIAIGGEEIHVMAGPCAVESREQLLEAARLVKEAGATLLRGGAFKPRTSPYSF 139 789****************************************************************** PP TIGR01361 71 qGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkr 139 qGl+eeglkll++a+++tgl+vvtev+d++ + ++aey+DilqiG+rnmqnf lL+ev+k +kPvlLkr lcl|NCBI__GCF_000215085.1:WP_013842920.1 140 QGLEEEGLKLLAEAREKTGLKVVTEVMDASTLPMIAEYADILQIGTRNMQNFFLLREVAKVDKPVLLKR 208 ********************************************************************* PP TIGR01361 140 glaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrr 208 g++atieewl+aaeYi++ gn nvilcerGirt+e+ tr+tldl+a++++k+l+hlP+ivDpsha G++ lcl|NCBI__GCF_000215085.1:WP_013842920.1 209 GVSATIEEWLMAAEYIMAGGNYNVILCERGIRTYESFTRNTLDLAAIPVVKHLSHLPIIVDPSHAIGKW 277 ********************************************************************* PP TIGR01361 209 dlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelka 259 +v+p+a aava+Gadgllievhp+P++al+D++q+ltp++f+ l+++lk+ lcl|NCBI__GCF_000215085.1:WP_013842920.1 278 RFVPPMAAAAVAAGADGLLIEVHPNPAEALCDGPQSLTPTNFQSLMQDLKS 328 ***********************************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (340 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 7.70 // [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