Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_009545461.1 CCE_RS15905 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000017845.1:WP_009545461.1 Length = 352 Score = 296 bits (757), Expect = 7e-85 Identities = 155/334 (46%), Positives = 225/334 (67%), Gaps = 8/334 (2%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLD-CV 59 MIVV+K GS ++I ++ + + L G+ + VIG++G+ + + + + + Sbjct: 1 MIVVMKVGSPADEIERISQEFTEWGLSPEKIVGKHKVVIGLVGETASLDPLQIQEISPWI 60 Query: 60 ESVVRVLKPYKLVSREF-HPE--DTVIDL--GDVKIGNGY-FTIIAGPCSVEGREMLMET 113 E+V+RV +P+K S E+ H E + +ID G V +G + ++AGPCSVE M++ET Sbjct: 61 ENVLRVEQPFKRASLEYRHGEYSEVIIDTPDGPVAVGKNHPVAVVAGPCSVENEAMIVET 120 Query: 114 AHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPK 173 A + G K LRGGAYKPRTSPY+FQG GE LE L A + G+ ++TE + DL K Sbjct: 121 AKRVKAAGAKFLRGGAYKPRTSPYAFQGHGESALELLAAAREASGLGIITEVMDAADLDK 180 Query: 174 VAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKII 233 +AE AD++Q+GARN QNF LL K G+ +KPVLLKRG TI+E+L++AEY+ +GN ++I Sbjct: 181 IAEVADVVQVGARNMQNFSLLKKVGAQDKPVLLKRGMSATIDEWLMAAEYVLAAGNPRVI 240 Query: 234 LCERGIRTFE-KATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGA 292 LCERGIRTF+ K TRNTLD+S +P++R +HLPI++DPSH G+ D V ++ AAIA G Sbjct: 241 LCERGIRTFDGKYTRNTLDLSVLPVLRSLTHLPIMIDPSHGTGKSDYVPAMAAAAIAAGT 300 Query: 293 HGIIVEVHPEPEKALSDGKQSLDFELFKELVQEM 326 +++EVHP P KALSDG QSL + F ++Q++ Sbjct: 301 DSLMIEVHPNPAKALSDGPQSLTPDKFDRVMQDL 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: 304 Number of extensions: 11 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: 352 Length adjustment: 29 Effective length of query: 309 Effective length of database: 323 Effective search space: 99807 Effective search space used: 99807 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_009545461.1 CCE_RS15905 (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.31564.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-124 398.9 0.0 5.6e-124 398.7 0.0 1.1 1 lcl|NCBI__GCF_000017845.1:WP_009545461.1 CCE_RS15905 3-deoxy-7-phosphohep Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017845.1:WP_009545461.1 CCE_RS15905 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 398.7 0.0 5.6e-124 5.6e-124 6 258 .. 76 335 .. 71 337 .. 0.95 Alignments for each domain: == domain 1 score: 398.7 bits; conditional E-value: 5.6e-124 TIGR01361 6 kvkkeetvvdved.....vkiGege.liviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPy 68 ++++ e+ + + d v++G+++ ++v+aGPCsve+e +ivetak+vk+aGak+lrGga+kPrtsPy lcl|NCBI__GCF_000017845.1:WP_009545461.1 76 EYRHGEYSEVIIDtpdgpVAVGKNHpVAVVAGPCSVENEAMIVETAKRVKAAGAKFLRGGAYKPRTSPY 144 5555544444333344779*****9889***************************************** PP TIGR01361 69 sfqGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlL 137 +fqG+ge++l+ll++a+++ gl ++tev+d++d++ +ae++D++q+Garnmqnf+lLk+vg+++kPvlL lcl|NCBI__GCF_000017845.1:WP_009545461.1 145 AFQGHGESALELLAAAREASGLGIITEVMDAADLDKIAEVADVVQVGARNMQNFSLLKKVGAQDKPVLL 213 ********************************************************************* PP TIGR01361 138 krglaatieewleaaeYilsegnenvilcerGirtfe.katrftldlsavallkklthlPvivDpshaa 205 krg++ati+ewl+aaeY+l++gn++vilcerGirtf+ k+tr+tldls++++l++lthlP+++Dpsh++ lcl|NCBI__GCF_000017845.1:WP_009545461.1 214 KRGMSATIDEWLMAAEYVLAAGNPRVILCERGIRTFDgKYTRNTLDLSVLPVLRSLTHLPIMIDPSHGT 282 *************************************99****************************** PP TIGR01361 206 GrrdlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelk 258 G++d+v+++a aa+a+G+d+l+ievhp+P+kalsD++q+ltp++f++++++l+ lcl|NCBI__GCF_000017845.1:WP_009545461.1 283 GKSDYVPAMAAAAIAAGTDSLMIEVHPNPAKALSDGPQSLTPDKFDRVMQDLS 335 **************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (352 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: 00:00:00.00 # Mc/sec: 9.38 // [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