Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011936974.1 GURA_RS00135 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000016745.1:WP_011936974.1 Length = 339 Score = 334 bits (857), Expect = 2e-96 Identities = 171/334 (51%), Positives = 231/334 (69%), Gaps = 2/334 (0%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDR-YVVADKFESLDCV 59 MI+V+K G+ ++D +V+K + K H+ G R VIG +GD+R V ES+ V Sbjct: 1 MIIVMKAGAVKKDKDEVLKRIKELGYKPHVIHGATRDVIGAVGDERGKAVLQSIESMHGV 60 Query: 60 ESVVRVLKPYKLVSREFHPEDTVIDLGD-VKIGNGYFTIIAGPCSVEGREMLMETAHFLS 118 E+VV +L+PYKL S+E E ++I + D + IG ++AGPCSVE E ++ +A + Sbjct: 61 ENVVPILQPYKLASKEVKKESSIIPITDTLSIGGKQLIVMAGPCSVESEEQIIASAMAVK 120 Query: 119 ELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYA 178 E G VLRGGA+KPRTSPYSFQGL E+GL+ L +A D G+ +VTE + + VAEYA Sbjct: 121 EAGAHVLRGGAFKPRTSPYSFQGLEEEGLKLLAKARDLTGLPIVTEVVNPETAELVAEYA 180 Query: 179 DIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERG 238 DI+QIGARNAQNF LL K G K VLLKRG TI+EFL+SAEYI + GN +ILCERG Sbjct: 181 DILQIGARNAQNFALLKKVGQLKKAVLLKRGMSMTIQEFLMSAEYIMSEGNQSVILCERG 240 Query: 239 IRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVE 298 IRTFE ATRNTLD+SA+P++++++HLPI+ DPSH G V P++ AA+A GA G+I+E Sbjct: 241 IRTFETATRNTLDLSAIPVLKEKTHLPIIADPSHGTGNYHYVAPMAYAAVAAGADGLIIE 300 Query: 299 VHPEPEKALSDGKQSLDFELFKELVQEMKKLADA 332 VHP+PE A SDG QSL F ++ +++ A+A Sbjct: 301 VHPDPEHASSDGPQSLKPAKFARMMAQLRLFAEA 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: 336 Number of extensions: 9 Number of successful extensions: 3 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_011936974.1 GURA_RS00135 (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.1176799.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-125 402.2 0.1 5.7e-125 401.9 0.1 1.1 1 NCBI__GCF_000016745.1:WP_011936974.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000016745.1:WP_011936974.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 401.9 0.1 5.7e-125 5.7e-125 2 258 .. 72 329 .. 71 331 .. 0.98 Alignments for each domain: == domain 1 score: 401.9 bits; conditional E-value: 5.7e-125 TIGR01361 2 laskkvkkeetvvdved.vkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysfqGl 73 lask+vkke++++ ++d ++iG+++liv+aGPCsveseeqi+++a avkeaGa++lrGgafkPrtsPysfqGl NCBI__GCF_000016745.1:WP_011936974.1 72 LASKEVKKESSIIPITDtLSIGGKQLIVMAGPCSVESEEQIIASAMAVKEAGAHVLRGGAFKPRTSPYSFQGL 144 789*****99998886649****************************************************** PP TIGR01361 74 geeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkrglaatie 146 +eeglkll++a+d tgl++vtev++++ e+vaey+DilqiGarn+qnf+lLk+vg+ kk vlLkrg++ ti+ NCBI__GCF_000016745.1:WP_011936974.1 145 EEEGLKLLAKARDLTGLPIVTEVVNPETAELVAEYADILQIGARNAQNFALLKKVGQLKKAVLLKRGMSMTIQ 217 ************************************************************************* PP TIGR01361 147 ewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrrdlvlplakaav 219 e+l++aeYi+segn+ vilcerGirtfe+atr+tldlsa+++lk++thlP+i+Dpsh++G+ ++v p+a aav NCBI__GCF_000016745.1:WP_011936974.1 218 EFLMSAEYIMSEGNQSVILCERGIRTFETATRNTLDLSAIPVLKEKTHLPIIADPSHGTGNYHYVAPMAYAAV 290 ************************************************************************* PP TIGR01361 220 avGadgllievhpdPekalsDseqqltpeefkelvkelk 258 a+Gadgl+ievhpdPe+a sD++q+l+p++f++++ +l+ NCBI__GCF_000016745.1:WP_011936974.1 291 AAGADGLIIEVHPDPEHASSDGPQSLKPAKFARMMAQLR 329 ***********************************9986 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 18.38 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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