Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_028990085.1 G579_RS0110100 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000423825.1:WP_028990085.1 Length = 338 Score = 331 bits (849), Expect = 1e-95 Identities = 166/335 (49%), Positives = 235/335 (70%), Gaps = 1/335 (0%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60 MI+VLK ++E +I++V+ ES L +S+G ER V+G IGD+R + FES+ VE Sbjct: 1 MIIVLKQQASEAEIQQVLDRIESLGLTPTVSRGAERVVVGAIGDERKLAEGAFESMAAVE 60 Query: 61 SVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSEL 120 V+ +LKPYKLVSREF DTVID+ V +G II+GPCSVE +E + +A + E Sbjct: 61 QVLPILKPYKLVSREFKATDTVIDVSGVPLGGNAVQIISGPCSVESQEQMDLSAKAVHEA 120 Query: 121 GVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYA-D 179 G +++RGGA+KPRTSPY+FQGLG+ GL+Y + AA KY + +VTE + + E D Sbjct: 121 GCRLMRGGAFKPRTSPYTFQGLGDIGLDYFKNAASKYNLPIVTELMDVRKIDLFLEKGVD 180 Query: 180 IIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGI 239 +IQIG RN QNF LL + G + P++LKRG TI+++L++AEYIA GN KII ERGI Sbjct: 181 VIQIGTRNMQNFDLLKEVGRLDVPIILKRGMSATIKDWLMAAEYIAAQGNQKIIFAERGI 240 Query: 240 RTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEV 299 RTFE RN LD++A+P+++KE+HLP+++DPSH+GG+ LV LSRAA+AVGA G+++E Sbjct: 241 RTFETYYRNVLDVTAIPVLKKETHLPVIIDPSHAGGKAWLVPALSRAAVAVGADGLLIET 300 Query: 300 HPEPEKALSDGKQSLDFELFKELVQEMKKLADALG 334 HP P +A D Q+L+ E K L+++++ +A LG Sbjct: 301 HPCPSEAWCDADQALNPEQLKTLMKDLRAIAQILG 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: 318 Number of extensions: 13 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: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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_028990085.1 G579_RS0110100 (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.1296.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-112 361.7 0.0 1.3e-112 361.4 0.0 1.1 1 lcl|NCBI__GCF_000423825.1:WP_028990085.1 G579_RS0110100 3-deoxy-7-phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000423825.1:WP_028990085.1 G579_RS0110100 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 361.4 0.0 1.3e-112 1.3e-112 2 259 .. 71 329 .. 70 330 .. 0.98 Alignments for each domain: == domain 1 score: 361.4 bits; conditional E-value: 1.3e-112 TIGR01361 2 laskkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysf 70 l+s+++k +tv+dv++v +G++ + +i GPCsves+eq+ +akav+eaG +l+rGgafkPrtsPy+f lcl|NCBI__GCF_000423825.1:WP_028990085.1 71 LVSREFKATDTVIDVSGVPLGGNAVQIISGPCSVESQEQMDLSAKAVHEAGCRLMRGGAFKPRTSPYTF 139 78******************************************************************* PP TIGR01361 71 qGlgeeglkllkrakdetgllvvtevlderdveiv.aeyvDilqiGarnmqnfelLkevgkskkPvlLk 138 qGlg gl + k+a+++++l++vte++d+r+++++ ++ vD++qiG+rnmqnf+lLkevg+ + P++Lk lcl|NCBI__GCF_000423825.1:WP_028990085.1 140 QGLGDIGLDYFKNAASKYNLPIVTELMDVRKIDLFlEKGVDVIQIGTRNMQNFDLLKEVGRLDVPIILK 208 *********************************872557****************************** PP TIGR01361 139 rglaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGr 207 rg++ati++wl+aaeYi+++gn+++i+ erGirtfe++ r+ ld++a+++lkk+thlPvi+Dpsha G+ lcl|NCBI__GCF_000423825.1:WP_028990085.1 209 RGMSATIKDWLMAAEYIAAQGNQKIIFAERGIRTFETYYRNVLDVTAIPVLKKETHLPVIIDPSHAGGK 277 ********************************************************************* PP TIGR01361 208 rdlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelka 259 lv++l++aavavGadgllie hp P +a++D++q l+pe++k+l+k+l+a lcl|NCBI__GCF_000423825.1:WP_028990085.1 278 AWLVPALSRAAVAVGADGLLIETHPCPSEAWCDADQALNPEQLKTLMKDLRA 329 ************************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (338 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.50 // [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