Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_014449220.1 LFE_RS05285 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000284315.1:WP_014449220.1 Length = 339 Score = 357 bits (917), Expect = e-103 Identities = 185/334 (55%), Positives = 240/334 (71%), Gaps = 1/334 (0%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60 MI+VLKP +T+ DI + + L HISKG ERT+IG IGDDR + VE Sbjct: 1 MIIVLKPEATQADIAHISGKLKEKGLAVHISKGSERTIIGAIGDDRLLAELPLAIFPGVE 60 Query: 61 SVVRVLKPYKLVSREFHPEDTVIDLGD-VKIGNGYFTIIAGPCSVEGREMLMETAHFLSE 119 SV ++L+P+KLVSREF E+T+I + V IG ++AGPC+VE E L+ A + E Sbjct: 61 SVHKILQPFKLVSREFKKENTIIRFPNGVTIGGEEIQVMAGPCAVESDEQLLFVAERVKE 120 Query: 120 LGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYAD 179 G K+LRGGA+KPRTSPY+FQGLGE GL++L +A +K G+ V+TE + DL V E+ D Sbjct: 121 SGAKILRGGAFKPRTSPYTFQGLGETGLKHLSKAREKTGLLVITELMDPRDLDMVEEHTD 180 Query: 180 IIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGI 239 IIQIGARN QNFRLLS G KPVLLKRG TI+EFL++AEYIA+ GN IILCERGI Sbjct: 181 IIQIGARNMQNFRLLSDVGRARKPVLLKRGLSATIKEFLMAAEYIASQGNQDIILCERGI 240 Query: 240 RTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEV 299 RTFE TRNTLD++AVP+++ +HLPILVDPSH GR DLVIP+++A IA GA +++EV Sbjct: 241 RTFETMTRNTLDLNAVPVLKSLTHLPILVDPSHGTGRWDLVIPMAKAGIAAGADALMIEV 300 Query: 300 HPEPEKALSDGKQSLDFELFKELVQEMKKLADAL 333 H PE+A SDG++SL E F+ L++E +K+A A+ Sbjct: 301 HNNPEEAFSDGEESLTPENFERLMRECRKVASAV 334 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: 347 Number of extensions: 11 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: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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_014449220.1 LFE_RS05285 (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.2665.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-127 410.9 0.0 1.3e-127 410.6 0.0 1.1 1 lcl|NCBI__GCF_000284315.1:WP_014449220.1 LFE_RS05285 3-deoxy-7-phosphohep Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000284315.1:WP_014449220.1 LFE_RS05285 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 410.6 0.0 1.3e-127 1.3e-127 2 258 .. 71 328 .. 70 330 .. 0.98 Alignments for each domain: == domain 1 score: 410.6 bits; conditional E-value: 1.3e-127 TIGR01361 2 laskkvkkeetvvdv.edvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPys 69 l+s+++kke+t+++ ++v+iG++e+ v+aGPC+ves eq++ +a++vke Gak+lrGgafkPrtsPy+ lcl|NCBI__GCF_000284315.1:WP_014449220.1 71 LVSREFKKENTIIRFpNGVTIGGEEIQVMAGPCAVESDEQLLFVAERVKESGAKILRGGAFKPRTSPYT 139 79*********9998356*************************************************** PP TIGR01361 70 fqGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLk 138 fqGlge glk l++a+++tgllv+te++d+rd+++v+e++Di+qiGarnmqnf+lL++vg+++kPvlLk lcl|NCBI__GCF_000284315.1:WP_014449220.1 140 FQGLGETGLKHLSKAREKTGLLVITELMDPRDLDMVEEHTDIIQIGARNMQNFRLLSDVGRARKPVLLK 208 ********************************************************************* PP TIGR01361 139 rglaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGr 207 rgl+ati+e+l+aaeYi+s+gn+++ilcerGirtfe++tr+tldl+av++lk+lthlP++vDpsh++Gr lcl|NCBI__GCF_000284315.1:WP_014449220.1 209 RGLSATIKEFLMAAEYIASQGNQDIILCERGIRTFETMTRNTLDLNAVPVLKSLTHLPILVDPSHGTGR 277 ********************************************************************* PP TIGR01361 208 rdlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelk 258 +dlv+p+aka++a+Gad+l+ievh++Pe+a+sD+e +ltpe+f++l++e++ lcl|NCBI__GCF_000284315.1:WP_014449220.1 278 WDLVIPMAKAGIAAGADALMIEVHNNPEEAFSDGEESLTPENFERLMRECR 328 ***********************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (339 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: 10.06 // [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