Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_012282982.1 HM1_RS08650 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000019165.1:WP_012282982.1 Length = 337 Score = 351 bits (900), Expect = e-101 Identities = 172/334 (51%), Positives = 234/334 (70%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60 MI+V+ G+T + I + + L+ H+S+G E+T+IG+IGD + A E+ VE Sbjct: 1 MIIVMSEGATAQQIEAIKQRLTKEGLQIHLSQGVEKTIIGVIGDKSRISASTLEAQPGVE 60 Query: 61 SVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSEL 120 V+ VL+PYKL R F E+TVI +GDV+IG + AGPC+VE RE L+E+A + Sbjct: 61 KVMPVLQPYKLAGRSFRHENTVIRIGDVEIGGDALQVFAGPCAVESREQLLESAQAVKAA 120 Query: 121 GVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADI 180 G ++LRGGA+KPRTSPY+FQGL E+GL+ L +A ++ G+ + TE + + +AEY+DI Sbjct: 121 GARILRGGAFKPRTSPYAFQGLEEQGLKLLAQAREETGLLICTEVMDTRSIEMIAEYSDI 180 Query: 181 IQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIR 240 +Q+G RN QNF LL + N+P+LLKRG TIEE+L++AEYI GN +ILCERGIR Sbjct: 181 LQVGTRNMQNFHLLRELSRVNRPILLKRGLSATIEEWLMAAEYIMAGGNYNVILCERGIR 240 Query: 241 TFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVH 300 TFE TRNTLD+SA+PII+ SHLPI+VDPSH G+R LV P+S AA+A GA GI+VEVH Sbjct: 241 TFETQTRNTLDLSAIPIIKSLSHLPIIVDPSHGTGKRHLVRPMSMAAVAAGADGIMVEVH 300 Query: 301 PEPEKALSDGKQSLDFELFKELVQEMKKLADALG 334 P P +AL DG QSL E F L+ E+++LA +G Sbjct: 301 PNPAEALCDGPQSLRPEEFASLMDELRRLAGVMG 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: 323 Number of extensions: 8 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_012282982.1 HM1_RS08650 (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.8803.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-130 417.9 0.0 9.8e-130 417.5 0.0 1.1 1 lcl|NCBI__GCF_000019165.1:WP_012282982.1 HM1_RS08650 3-deoxy-7-phosphohep Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019165.1:WP_012282982.1 HM1_RS08650 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.5 0.0 9.8e-130 9.8e-130 2 258 .. 71 327 .. 70 329 .. 0.99 Alignments for each domain: == domain 1 score: 417.5 bits; conditional E-value: 9.8e-130 TIGR01361 2 laskkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysf 70 la +++++e+tv+++ dv+iG++ l v aGPC+ves+eq++e+a+avk+aGa++lrGgafkPrtsPy+f lcl|NCBI__GCF_000019165.1:WP_012282982.1 71 LAGRSFRHENTVIRIGDVEIGGDALQVFAGPCAVESREQLLESAQAVKAAGARILRGGAFKPRTSPYAF 139 67899**************************************************************** PP TIGR01361 71 qGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkr 139 qGl+e+glkll++a++etgll+ tev+d+r +e++aey Dilq+G+rnmqnf+lL+e+++ ++P+lLkr lcl|NCBI__GCF_000019165.1:WP_012282982.1 140 QGLEEQGLKLLAQAREETGLLICTEVMDTRSIEMIAEYSDILQVGTRNMQNFHLLRELSRVNRPILLKR 208 ********************************************************************* PP TIGR01361 140 glaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrr 208 gl+atieewl+aaeYi++ gn nvilcerGirtfe++tr+tldlsa++++k+l+hlP+ivDpsh++G+r lcl|NCBI__GCF_000019165.1:WP_012282982.1 209 GLSATIEEWLMAAEYIMAGGNYNVILCERGIRTFETQTRNTLDLSAIPIIKSLSHLPIIVDPSHGTGKR 277 ********************************************************************* PP TIGR01361 209 dlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelk 258 +lv p+++aava+Gadg+++evhp+P++al+D++q+l+peef+ l++el+ lcl|NCBI__GCF_000019165.1:WP_012282982.1 278 HLVRPMSMAAVAAGADGIMVEVHPNPAEALCDGPQSLRPEEFASLMDELR 327 ***********************************************987 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.72 // [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