Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_013260004.1 DEBA_RS16065 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000143965.1:WP_013260004.1 Length = 346 Score = 309 bits (792), Expect = 6e-89 Identities = 161/342 (47%), Positives = 228/342 (66%), Gaps = 12/342 (3%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGII--------GDDRYVVADK 52 M+V ++ G + + V+ E LK I + V+G++ D R+V++D Sbjct: 1 MVVSMREGCPKSQVAAVIAAMERRGLKVRIISPGPKVVLGVVEAVSKHLTDDLRFVLSD- 59 Query: 53 FESLDCVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLME 112 + VE V +KLV R + +V+ +G IG +IAGPC+VE RE L++ Sbjct: 60 ---MPGVEEVSDFHTDWKLVWRGPEQQTSVVRMGGRSIGGPELMVIAGPCAVECRENLLQ 116 Query: 113 TAHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLP 172 TA ++ G +RGGA+KPRTSPYSF+GLGE+GL+YL EA + G+ VVTE + ++ Sbjct: 117 TAQAVAASGAGAIRGGAFKPRTSPYSFRGLGEEGLKYLAEARELTGLPVVTEVMSFHEVE 176 Query: 173 KVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKI 232 VA YAD++QIGARN QNF LL AG +KPVLLKRG NT++E LL AEYI GN ++ Sbjct: 177 LVARYADVLQIGARNMQNFALLEAAGEVDKPVLLKRGLGNTVKELLLCAEYILARGNQQV 236 Query: 233 ILCERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGA 292 + CERGIRTFE TRNTLD++AVPI+++ SHLP++VDPSH+ G+R+LV L+ AA+A GA Sbjct: 237 MFCERGIRTFETETRNTLDLAAVPILKQNSHLPVVVDPSHAAGKRELVPALALAAVAAGA 296 Query: 293 HGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALG 334 G+++EVHPEP KALSDG+Q++D F +L++ + +A A+G Sbjct: 297 DGLMIEVHPEPAKALSDGRQTIDLPAFDDLMKRLALVAQAVG 338 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: 316 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: 346 Length adjustment: 29 Effective length of query: 309 Effective length of database: 317 Effective search space: 97953 Effective search space used: 97953 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_013260004.1 DEBA_RS16065 (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.17539.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-118 379.4 0.0 5.3e-118 379.1 0.0 1.1 1 lcl|NCBI__GCF_000143965.1:WP_013260004.1 DEBA_RS16065 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000143965.1:WP_013260004.1 DEBA_RS16065 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 379.1 0.0 5.3e-118 5.3e-118 9 258 .. 82 331 .. 75 333 .. 0.98 Alignments for each domain: == domain 1 score: 379.1 bits; conditional E-value: 5.3e-118 TIGR01361 9 keetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysfqGlgeeg 77 ++++vv++ + +iG+ el+viaGPC+ve +e++++ta+av + Ga +rGgafkPrtsPysf+Glgeeg lcl|NCBI__GCF_000143965.1:WP_013260004.1 82 QQTSVVRMGGRSIGGPELMVIAGPCAVECRENLLQTAQAVAASGAGAIRGGAFKPRTSPYSFRGLGEEG 150 5678999************************************************************** PP TIGR01361 78 lkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkrglaatie 146 lk+l++a++ tgl+vvtev+ ++ve+va+y+D+lqiGarnmqnf+lL+++g+ +kPvlLkrgl++t++ lcl|NCBI__GCF_000143965.1:WP_013260004.1 151 LKYLAEARELTGLPVVTEVMSFHEVELVARYADVLQIGARNMQNFALLEAAGEVDKPVLLKRGLGNTVK 219 ********************************************************************* PP TIGR01361 147 ewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrrdlvlpla 215 e+l +aeYil++gn++v++cerGirtfe+ tr+tldl+av++lk+ +hlPv+vDpshaaG+r+lv++la lcl|NCBI__GCF_000143965.1:WP_013260004.1 220 ELLLCAEYILARGNQQVMFCERGIRTFETETRNTLDLAAVPILKQNSHLPVVVDPSHAAGKRELVPALA 288 ********************************************************************* PP TIGR01361 216 kaavavGadgllievhpdPekalsDseqqltpeefkelvkelk 258 aava+Gadgl+ievhp+P+kalsD++q ++ f+ l+k+l+ lcl|NCBI__GCF_000143965.1:WP_013260004.1 289 LAAVAAGADGLMIEVHPEPAKALSDGRQTIDLPAFDDLMKRLA 331 ***************************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (346 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: 00:00:00.00 # Mc/sec: 12.21 // [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