Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011460211.1 DHAF_RS16945 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000021925.1:WP_011460211.1 Length = 342 Score = 354 bits (908), Expect = e-102 Identities = 177/334 (52%), Positives = 241/334 (72%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60 MI+VLK G+ E +++++ + K H+S+G E+ +IG +GD + A E+L VE Sbjct: 1 MIIVLKRGAGEAEVQEINERLSQEGFKIHLSQGVEKIIIGAVGDRSRLKALDLEALPWVE 60 Query: 61 SVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSEL 120 VV +L PYKLVSREF +T+I +GD +IG ++AGPCSVE R ++ETAH + E Sbjct: 61 KVVPILAPYKLVSREFQSGNTIIKIGDYEIGGEEIHVMAGPCSVESRAQIIETAHAVKEA 120 Query: 121 GVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADI 180 G LRGGA+KPRTSPY+FQGL E+GL+ L EA ++ G+ V+TE + D+ VA YADI Sbjct: 121 GATFLRGGAFKPRTSPYAFQGLEEEGLKLLAEAREETGLLVITEVVDVRDVELVAHYADI 180 Query: 181 IQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIR 240 +QIGARN QNF LL + NKP+LLKRG T+EE++++AEYI + GN +++ CERGIR Sbjct: 181 LQIGARNMQNFFLLKEVAKTNKPILLKRGPSATLEEWMMAAEYIMDGGNYQVMFCERGIR 240 Query: 241 TFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVH 300 TFE TRNTLD+S VP ++ SHLP++VDPSH GR +LV P+++AA+A GA GIIVEVH Sbjct: 241 TFETYTRNTLDLSMVPALQSLSHLPVIVDPSHGTGRWNLVPPMAKAAVAAGADGIIVEVH 300 Query: 301 PEPEKALSDGKQSLDFELFKELVQEMKKLADALG 334 P+PEKA+SDGKQSL + F ++ E++ LA ALG Sbjct: 301 PQPEKAVSDGKQSLTPDNFASMMAELEILAQALG 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: 312 Number of extensions: 7 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: 342 Length adjustment: 28 Effective length of query: 310 Effective length of database: 314 Effective search space: 97340 Effective search space used: 97340 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_011460211.1 DHAF_RS16945 (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.2854.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-128 413.4 0.0 2.7e-128 412.8 0.0 1.2 1 lcl|NCBI__GCF_000021925.1:WP_011460211.1 DHAF_RS16945 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_011460211.1 DHAF_RS16945 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.8 0.0 2.7e-128 2.7e-128 2 258 .. 71 327 .. 70 329 .. 0.99 Alignments for each domain: == domain 1 score: 412.8 bits; conditional E-value: 2.7e-128 TIGR01361 2 laskkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysf 70 l+s++++ +t++++ d +iG++e+ v+aGPCsves+ qi+eta+avkeaGa++lrGgafkPrtsPy+f lcl|NCBI__GCF_000021925.1:WP_011460211.1 71 LVSREFQSGNTIIKIGDYEIGGEEIHVMAGPCSVESRAQIIETAHAVKEAGATFLRGGAFKPRTSPYAF 139 789****************************************************************** PP TIGR01361 71 qGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkr 139 qGl+eeglkll++a++etgllv+tev+d+rdve+va+y+DilqiGarnmqnf lLkev+k++kP+lLkr lcl|NCBI__GCF_000021925.1:WP_011460211.1 140 QGLEEEGLKLLAEAREETGLLVITEVVDVRDVELVAHYADILQIGARNMQNFFLLKEVAKTNKPILLKR 208 ********************************************************************* PP TIGR01361 140 glaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrr 208 g++at+eew++aaeYi+ gn +v++cerGirtfe++tr+tldls v++l++l+hlPvivDpsh++Gr+ lcl|NCBI__GCF_000021925.1:WP_011460211.1 209 GPSATLEEWMMAAEYIMDGGNYQVMFCERGIRTFETYTRNTLDLSMVPALQSLSHLPVIVDPSHGTGRW 277 ********************************************************************* PP TIGR01361 209 dlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelk 258 +lv+p+akaava+Gadg+++evhp+Peka+sD++q+ltp++f+ ++ el+ lcl|NCBI__GCF_000021925.1:WP_011460211.1 278 NLVPPMAKAAVAAGADGIIVEVHPQPEKAVSDGKQSLTPDNFASMMAELE 327 **********************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (342 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: 00:00:00.00 # Mc/sec: 10.37 // [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