Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_018306370.1 DHAF_RS05785 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9YEJ7 (270 letters) >NCBI__GCF_000021925.1:WP_018306370.1 Length = 319 Score = 294 bits (752), Expect = 2e-84 Identities = 153/263 (58%), Positives = 189/263 (71%) Query: 3 GFKGVKLALKSEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHM 62 GF + L L + + + + IG ++AGPC+VES EQ+R AA VK AG + Sbjct: 41 GFGVMNLPLVGLKDERSTIRIGDTTIGAREVVLMAGPCAVESGEQMRAAAQGVKAAGGKI 100 Query: 63 LRGGAFKPRTSPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIG 122 LRGG +KPRTSPYSFQGLG EG+ LR A E GL VTEV+D R ++ + D+LQ+G Sbjct: 101 LRGGVYKPRTSPYSFQGLGEEGIDYLREAAAEYGLLTVTEVMDERSLDVLVDKVDILQVG 160 Query: 123 ARNMQNFPLLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEP 182 +RNMQNF LL+ +G PV+LKRG TVEE LAAAEYIL GN QV+L ERGIRTFEP Sbjct: 161 SRNMQNFHLLKLLGEVRNPVILKRGLAATVEEWLAAAEYILAGGNAQVILCERGIRTFEP 220 Query: 183 STRFTLDVAAVAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEVHPNPE 242 STR TLD++AV+++K +HLPVIVDPSH AGR ++PALAKA +A GADGL++EVHP+PE Sbjct: 221 STRNTLDLSAVSLVKVLSHLPVIVDPSHAAGRVDIIPALAKAAVAVGADGLLIEVHPHPE 280 Query: 243 EALSDAKQQLTPGEFARLMGELR 265 EA SD Q LTP +FARL ELR Sbjct: 281 EAQSDGMQSLTPEQFARLAAELR 303 Lambda K H 0.318 0.136 0.392 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: 217 Number of extensions: 6 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: 270 Length of database: 319 Length adjustment: 26 Effective length of query: 244 Effective length of database: 293 Effective search space: 71492 Effective search space used: 71492 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: 48 (23.1 bits)
Align candidate WP_018306370.1 DHAF_RS05785 (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.21716.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-120 385.1 0.0 9.4e-120 384.8 0.0 1.0 1 lcl|NCBI__GCF_000021925.1:WP_018306370.1 DHAF_RS05785 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_018306370.1 DHAF_RS05785 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 384.8 0.0 9.4e-120 9.4e-120 8 258 .. 53 303 .. 50 305 .. 0.98 Alignments for each domain: == domain 1 score: 384.8 bits; conditional E-value: 9.4e-120 TIGR01361 8 kkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysfqGlgee 76 k e++ +++ d +iG e++++aGPC+ves eq++++a+ vk+aG k+lrGg++kPrtsPysfqGlgee lcl|NCBI__GCF_000021925.1:WP_018306370.1 53 KDERSTIRIGDTTIGAREVVLMAGPCAVESGEQMRAAAQGVKAAGGKILRGGVYKPRTSPYSFQGLGEE 121 567788999************************************************************ PP TIGR01361 77 glkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkrglaati 145 g+ +l++a++e+gll+vtev+der ++++ + vDilq+G+rnmqnf+lLk +g+ + Pv+Lkrglaat+ lcl|NCBI__GCF_000021925.1:WP_018306370.1 122 GIDYLREAAAEYGLLTVTEVMDERSLDVLVDKVDILQVGSRNMQNFHLLKLLGEVRNPVILKRGLAATV 190 ********************************************************************* PP TIGR01361 146 eewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrrdlvlpl 214 eewl+aaeYil+ gn +vilcerGirtfe +tr+tldlsav l+k l+hlPvivDpshaaGr d++++l lcl|NCBI__GCF_000021925.1:WP_018306370.1 191 EEWLAAAEYILAGGNAQVILCERGIRTFEPSTRNTLDLSAVSLVKVLSHLPVIVDPSHAAGRVDIIPAL 259 ********************************************************************* PP TIGR01361 215 akaavavGadgllievhpdPekalsDseqqltpeefkelvkelk 258 akaavavGadgllievhp+Pe+a sD+ q+ltpe+f++l el+ lcl|NCBI__GCF_000021925.1:WP_018306370.1 260 AKAAVAVGADGLLIEVHPHPEEAQSDGMQSLTPEQFARLAAELR 303 **************************************998875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (319 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: 9.20 // [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