Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_010532354.1 ON01_RS17690 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000224785.1:WP_010532354.1 Length = 360 Score = 548 bits (1413), Expect = e-161 Identities = 272/350 (77%), Positives = 313/350 (89%), Gaps = 1/350 (0%) Query: 1 MSNTELELLRQKADELNLQILKLINERGNVVKEIGKAKEAQGVNRFDPVRERTMLNNIIE 60 MSN ELE LRQ+ D +N ++L LIN+R +V++IG+ KE Q +NRFDPVRER MLN + + Sbjct: 1 MSN-ELEQLRQQLDGVNNELLDLINQRAEIVQQIGQVKEKQSINRFDPVRERKMLNELTQ 59 Query: 61 NNDGPFENSTIQHIFKEIFKAGLELQEEDHSKALLVSRKKKPEDTIVDIKGEKIGDGQQR 120 N+GPFENSTI+HIFKEIFKA LELQE+DH KALLVSRK+KPEDT++DIKGEK+GDG Sbjct: 60 KNNGPFENSTIEHIFKEIFKASLELQEDDHRKALLVSRKRKPEDTVIDIKGEKVGDGNLH 119 Query: 121 FIVGPCAVESYEQVAEVAAAAKKQGIKILRGGAFKPRTSPYDFQGLGVEGLQILKRVADE 180 I+GPC+VE+YEQV+EVA + K++G+K+LRGGAFKPRTSPYDFQGLGVEGLQILKRVADE Sbjct: 120 HIMGPCSVENYEQVSEVAKSVKQKGLKMLRGGAFKPRTSPYDFQGLGVEGLQILKRVADE 179 Query: 181 FDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRGLAATISE 240 DLAV+SEIV PAH+E+ALDY+DVIQIGARNMQNFELLKAAG KPVLLKRGL+ATISE Sbjct: 180 QDLAVVSEIVNPAHVEKALDYVDVIQIGARNMQNFELLKAAGETNKPVLLKRGLSATISE 239 Query: 241 FINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQETHLPVFVDVTHSTGR 300 F+NAAEYI S+GN IILCERGIRTYE ATRNTLDISAVPILKQETHLPV VDVTHSTGR Sbjct: 240 FVNAAEYINSRGNGDIILCERGIRTYEKATRNTLDISAVPILKQETHLPVMVDVTHSTGR 299 Query: 301 RDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIPEFEKWLNEL 350 RD+LLP AKAA+AIGADGVMAEVHPDP+VALSD+AQQM IP FE ++NEL Sbjct: 300 RDILLPAAKAAVAIGADGVMAEVHPDPAVALSDAAQQMDIPTFENFMNEL 349 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: 474 Number of extensions: 14 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: 360 Length adjustment: 29 Effective length of query: 329 Effective length of database: 331 Effective search space: 108899 Effective search space used: 108899 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_010532354.1 ON01_RS17690 (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.3419331.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-46 142.7 4.3 3.5e-46 141.9 4.3 1.4 1 NCBI__GCF_000224785.1:WP_010532354.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010532354.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 141.9 4.3 3.5e-46 3.5e-46 1 102 [] 1 101 [. 1 101 [. 0.99 Alignments for each domain: == domain 1 score: 141.9 bits; conditional E-value: 3.5e-46 TIGR01801 1 msnqeleslraevdelnrqilkliskrGevvkkiGkakeaqGvnrydParekemlneliesnkGPfedatikq 73 msn ele+lr+++d +n+++l+li++r e+v++iG+ ke+q nr+dP+re++mlnel ++n+GPfe++ti++ NCBI__GCF_000224785.1:WP_010532354.1 1 MSN-ELEQLRQQLDGVNNELLDLINQRAEIVQQIGQVKEKQSINRFDPVRERKMLNELTQKNNGPFENSTIEH 72 888.9******************************************************************** PP TIGR01801 74 ifkeifkaslelqesedkkallvsrkvkp 102 ifkeifkaslelqe++++kallvsrk kp NCBI__GCF_000224785.1:WP_010532354.1 73 IFKEIFKASLELQEDDHRKALLVSRKRKP 101 ***************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (102 nodes) Target sequences: 1 (360 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: 24.35 // [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