Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_078430109.1 BK574_RS22060 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_002019605.1:WP_078430109.1 Length = 358 Score = 553 bits (1424), Expect = e-162 Identities = 276/351 (78%), Positives = 316/351 (90%) Query: 1 MSNTELELLRQKADELNLQILKLINERGNVVKEIGKAKEAQGVNRFDPVRERTMLNNIIE 60 MSN +LE LR K DE+NLQ+L+LINER +V+EIGK K QGVNRFDPVRER MLN I E Sbjct: 1 MSNEQLETLRDKLDEVNLQLLELINERARLVQEIGKVKNKQGVNRFDPVRERKMLNLIAE 60 Query: 61 NNDGPFENSTIQHIFKEIFKAGLELQEEDHSKALLVSRKKKPEDTIVDIKGEKIGDGQQR 120 NN+GPFE ST+QH+FK+IFKAGLELQE+D+ KALLVSRKK PEDT++++KGE+IGDGQQR Sbjct: 61 NNNGPFETSTLQHLFKQIFKAGLELQEDDNRKALLVSRKKHPEDTVINLKGEQIGDGQQR 120 Query: 121 FIVGPCAVESYEQVAEVAAAAKKQGIKILRGGAFKPRTSPYDFQGLGVEGLQILKRVADE 180 ++GPCAVESYEQVA VA A K+QG+K+LRGGAFKPRTSPYDFQGLG+EGLQILKRVADE Sbjct: 121 LVMGPCAVESYEQVAAVAKAMKEQGMKLLRGGAFKPRTSPYDFQGLGLEGLQILKRVADE 180 Query: 181 FDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRGLAATISE 240 +D+AVISEIV P IE AL+YIDVIQIGARNM NFELLKAAG+V KPVLLKRGL+ATI E Sbjct: 181 YDMAVISEIVRPEDIEVALEYIDVIQIGARNMHNFELLKAAGSVNKPVLLKRGLSATIEE 240 Query: 241 FINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQETHLPVFVDVTHSTGR 300 FINAAEY++S+GN I+LCERGIRTYE ATRNTLDISAVPILKQETHLPV VDVTHSTGR Sbjct: 241 FINAAEYVISKGNGNIMLCERGIRTYEKATRNTLDISAVPILKQETHLPVLVDVTHSTGR 300 Query: 301 RDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIPEFEKWLNELK 351 +DLLLPTAKAALAIGAD VMAEVHPDP+VALSDSAQQM I +F ++++ L+ Sbjct: 301 KDLLLPTAKAALAIGADAVMAEVHPDPAVALSDSAQQMDIGQFNEFVSNLR 351 Lambda K H 0.316 0.134 0.369 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: 464 Number of extensions: 15 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: 358 Length of database: 358 Length adjustment: 29 Effective length of query: 329 Effective length of database: 329 Effective search space: 108241 Effective search space used: 108241 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_078430109.1 BK574_RS22060 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR01801 (aroA: chorismate mutase (EC 5.4.99.5))
# 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/TIGR01801.hmm # target sequence database: /tmp/gapView.22198.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01801 [M=102] Accession: TIGR01801 Description: CM_A: chorismate mutase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-46 140.9 2.9 1.2e-45 140.2 2.9 1.4 1 lcl|NCBI__GCF_002019605.1:WP_078430109.1 BK574_RS22060 3-deoxy-7-phosphoh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078430109.1 BK574_RS22060 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 140.2 2.9 1.2e-45 1.2e-45 1 102 [] 1 102 [. 1 102 [. 0.99 Alignments for each domain: == domain 1 score: 140.2 bits; conditional E-value: 1.2e-45 TIGR01801 1 msnqeleslraevdelnrqilkliskrGevvkkiGkakeaqGvnrydParekemlneliesnkGPfeda 69 msn++le+lr ++de+n+q+l+li++r +v++iGk k++qGvnr+dP+re++mln + e+n+GPfe++ lcl|NCBI__GCF_002019605.1:WP_078430109.1 1 MSNEQLETLRDKLDEVNLQLLELINERARLVQEIGKVKNKQGVNRFDPVRERKMLNLIAENNNGPFETS 69 9******************************************************************** PP TIGR01801 70 tikqifkeifkaslelqesedkkallvsrkvkp 102 t++++fk+ifka+lelqe++++kallvsrk+ p lcl|NCBI__GCF_002019605.1:WP_078430109.1 70 TLQHLFKQIFKAGLELQEDDNRKALLVSRKKHP 102 ******************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (102 nodes) Target sequences: 1 (358 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: 13.40 // [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