Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_017600011.1 D471_RS0118605 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000341125.1:WP_017600011.1 Length = 348 Score = 345 bits (885), Expect = e-99 Identities = 176/339 (51%), Positives = 237/339 (69%), Gaps = 17/339 (5%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDC-- 58 M++V+ P +T ++I +V+L S + ++++G RT+IG++GD ++F+ L Sbjct: 1 MVIVMAPDATSDNIDDLVELVSSAGGEAYVTRGVSRTIIGLVGD-----VERFQDLGLAA 55 Query: 59 ---VESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAH 115 V V+R+ PYKLVSRE H +V+++ V IG + T+IAGPC+VE E +E A Sbjct: 56 KPGVSDVLRISAPYKLVSRENHSSRSVVNVRGVPIGGEHMTVIAGPCAVETPEQTLEAAR 115 Query: 116 FLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVA 175 G +LRGGAYKPRTSPY+FQGLGE+GL L + ++ G+ +VTE + D+ VA Sbjct: 116 MALTAGASLLRGGAYKPRTSPYAFQGLGEEGLRILADVREETGLPIVTEVVDAADVELVA 175 Query: 176 EYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILC 235 YAD++QIG RN QNF LL AG KPVLLKRG TIEE+L++AEYIA GN I+LC Sbjct: 176 SYADMLQIGTRNMQNFALLQAAGDAGKPVLLKRGMSATIEEWLMAAEYIAQRGNLDIVLC 235 Query: 236 ERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGI 295 ERGIRTFEKATRNTLDISAVP+ + SHLP++VDPSHSGG+R+LV+PLSRAAIA+GA G+ Sbjct: 236 ERGIRTFEKATRNTLDISAVPVAQNLSHLPVIVDPSHSGGKRELVLPLSRAAIAIGADGV 295 Query: 296 IVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALG 334 IV+VHP+PE AL DG Q+L L +++ +L D G Sbjct: 296 IVDVHPDPENALCDGPQAL-------LEEDLAELRDVAG 327 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: 330 Number of extensions: 7 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: 348 Length adjustment: 29 Effective length of query: 309 Effective length of database: 319 Effective search space: 98571 Effective search space used: 98571 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_017600011.1 D471_RS0118605 (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.27570.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-122 394.4 0.0 1.4e-122 394.1 0.0 1.1 1 lcl|NCBI__GCF_000341125.1:WP_017600011.1 D471_RS0118605 3-deoxy-7-phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000341125.1:WP_017600011.1 D471_RS0118605 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 394.1 0.0 1.4e-122 1.4e-122 2 253 .. 71 322 .. 70 329 .. 0.98 Alignments for each domain: == domain 1 score: 394.1 bits; conditional E-value: 1.4e-122 TIGR01361 2 laskkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysf 70 l+s++ + +++vv+v++v iG+++++viaGPC+ve eq++e+a++ +aGa+llrGga+kPrtsPy+f lcl|NCBI__GCF_000341125.1:WP_017600011.1 71 LVSRENHSSRSVVNVRGVPIGGEHMTVIAGPCAVETPEQTLEAARMALTAGASLLRGGAYKPRTSPYAF 139 7899***************************************************************** PP TIGR01361 71 qGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkr 139 qGlgeegl++l+ +++etgl++vtev+d++dve+va+y+D+lqiG+rnmqnf+lL+++g + kPvlLkr lcl|NCBI__GCF_000341125.1:WP_017600011.1 140 QGLGEEGLRILADVREETGLPIVTEVVDAADVELVASYADMLQIGTRNMQNFALLQAAGDAGKPVLLKR 208 ********************************************************************* PP TIGR01361 140 glaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrr 208 g++atieewl+aaeYi+++gn +++lcerGirtfekatr+tld+sav+++++l+hlPvivDpsh+ G+r lcl|NCBI__GCF_000341125.1:WP_017600011.1 209 GMSATIEEWLMAAEYIAQRGNLDIVLCERGIRTFEKATRNTLDISAVPVAQNLSHLPVIVDPSHSGGKR 277 ********************************************************************* PP TIGR01361 209 dlvlplakaavavGadgllievhpdPekalsDseqqltpeefkel 253 +lvlpl++aa+a+Gadg++++vhpdPe+al+D++q l +e+++el lcl|NCBI__GCF_000341125.1:WP_017600011.1 278 ELVLPLSRAAIAIGADGVIVDVHPDPENALCDGPQALLEEDLAEL 322 ***************************************999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (348 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: 00:00:00.01 # Mc/sec: 8.20 // [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