Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011951238.1 SWIT_RS01945 3-deoxy-7-phosphoheptulonate synthase class II
Query= BRENDA::P29976 (525 letters) >NCBI__GCF_000016765.1:WP_011951238.1 Length = 458 Score = 550 bits (1416), Expect = e-161 Identities = 270/456 (59%), Positives = 337/456 (73%), Gaps = 2/456 (0%) Query: 72 ALKWTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKA 131 A WTP SW+ ++A+Q+PDYP+A L + + + +FPP+VFAGEAR L LA A GKA Sbjct: 2 ATNWTPASWRQQQAVQMPDYPDAAALAAAEQELSSFPPLVFAGEARELTASLAQVAAGKA 61 Query: 132 FLLQGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAF 191 FLLQGGDCAESF EF+ NIRDTFRVLLQM++VLTF ++PV+KVGRMAGQFAKPRS Sbjct: 62 FLLQGGDCAESFAEFHPNNIRDTFRVLLQMAVVLTFASKLPVVKVGRMAGQFAKPRSAPT 121 Query: 192 EEKDGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQR 251 EE GV LPSY+GD IN F E+SRIPDP RM+RAY+QSAATLNLLRAFA GGYA + + Sbjct: 122 EEIGGVTLPSYRGDIINDIGFSEESRIPDPRRMVRAYSQSAATLNLLRAFAQGGYANLHQ 181 Query: 252 VTQWNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTDH-PLMTTTDFYTSHECLLLP 310 V W LDF+ +S A +Y E+A R+ +AL FM+ACG+ + P + T FYTSHE LLLP Sbjct: 182 VHAWTLDFMGRSPWAAQYGEVAARIGDALDFMAACGINPETVPQLKGTQFYTSHEALLLP 241 Query: 311 YEQSLTRLDS-TSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFE 369 YEQ++TR DS +G Y+D SAH +W G+RTR AHVE+LRG+ NP+G+K ++P Sbjct: 242 YEQAMTREDSLNTGQYFDTSAHFLWIGDRTRFEGSAHVEYLRGVGNPIGLKCGPSLEPDA 301 Query: 370 LVKLVEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKA 429 L++L++ L+P +PGRIT+I R G + + LP L+RAV+R G+ V W CDPMHGN +KA Sbjct: 302 LLRLLDTLDPQRQPGRITLITRYGHDKIEKHLPALVRAVKREGRPVVWSCDPMHGNVVKA 361 Query: 430 PCGLKTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSR 489 G KTR FD ILAEVR F VH EG+H GGIH EMTGQNVTEC GG+ VT ++L+ R Sbjct: 362 ANGYKTRPFDRILAEVRGFFAVHRAEGTHGGGIHAEMTGQNVTECTGGAMAVTDENLADR 421 Query: 490 YHTHCDPRLNASQSLELAFIVAERLRKRRTGSQRVS 525 YHTHCDPRLNA QSLELAF++AE L + R + Sbjct: 422 YHTHCDPRLNAGQSLELAFLLAEMLNQEMKERDRAA 457 Lambda K H 0.318 0.132 0.389 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: 657 Number of extensions: 19 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: 525 Length of database: 458 Length adjustment: 34 Effective length of query: 491 Effective length of database: 424 Effective search space: 208184 Effective search space used: 208184 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: 52 (24.6 bits)
Align candidate WP_011951238.1 SWIT_RS01945 (3-deoxy-7-phosphoheptulonate synthase class II)
to HMM TIGR01358 (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/TIGR01358.hmm # target sequence database: /tmp/gapView.14889.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01358 [M=443] Accession: TIGR01358 Description: DAHP_synth_II: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-219 713.4 0.0 5.1e-219 713.2 0.0 1.0 1 lcl|NCBI__GCF_000016765.1:WP_011951238.1 SWIT_RS01945 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016765.1:WP_011951238.1 SWIT_RS01945 3-deoxy-7-phosphoheptulonate synthase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 713.2 0.0 5.1e-219 5.1e-219 1 441 [. 5 448 .. 5 450 .. 0.99 Alignments for each domain: == domain 1 score: 713.2 bits; conditional E-value: 5.1e-219 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 w+++swr+++a+q+P+yPda+al a +++l+s+PPlv+age+++l ++la+va+G+afllqgGdcaesf lcl|NCBI__GCF_000016765.1:WP_011951238.1 5 WTPASWRQQQAVQMPDYPDAAALAAAEQELSSFPPLVFAGEARELTASLAQVAAGKAFLLQGGDCAESF 73 89******************************************************************* PP TIGR01358 70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138 e++ +nird++rvllqmavvlt++++lPvvkvgr+aGq+akPrs+p+e+ +gvtlpsyrGd+in f lcl|NCBI__GCF_000016765.1:WP_011951238.1 74 AEFHPNNIRDTFRVLLQMAVVLTFASKLPVVKVGRMAGQFAKPRSAPTEEIGGVTLPSYRGDIINDIGF 142 ********************************************************************* PP TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207 +e++r+pdp+r+vray++saatlnllra+++gGya+l++vh+W+l+f+++sp +a+y ++a +i++al lcl|NCBI__GCF_000016765.1:WP_011951238.1 143 SEESRIPDPRRMVRAYSQSAATLNLLRAFAQGGYANLHQVHAWTLDFMGRSPWAAQYGEVAARIGDALD 211 ********************************************************************* PP TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvds.kegqlfdlsahllWiGertrqldgahve 273 fm a+g+++++ +lk +++ytshealll+ye+a+tr+ds ++gq+fd+sah+lWiG+rtr ahve lcl|NCBI__GCF_000016765.1:WP_011951238.1 212 FMAACGINPETvpQLKGTQFYTSHEALLLPYEQAMTREDSlNTGQYFDTSAHFLWIGDRTRFEGSAHVE 280 ********999999*************************97899************************* PP TIGR01358 274 flrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvW 342 +lrgv nPig+k+gps+e+d ll+l++ ldP+++PGr+tli+r G +ki ++lP l++avk++Gr vvW lcl|NCBI__GCF_000016765.1:WP_011951238.1 281 YLRGVGNPIGLKCGPSLEPDALLRLLDTLDPQRQPGRITLITRYGHDKIEKHLPALVRAVKREGRPVVW 349 ********************************************************************* PP TIGR01358 343 vtdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdl 411 +dpmhGn ++aa+Gyktr fd+il+ev++ff+vh+aeGth GG+h e+tG++vtec+GGa ++t+++l lcl|NCBI__GCF_000016765.1:WP_011951238.1 350 SCDPMHGNVVKAANGYKTRPFDRILAEVRGFFAVHRAEGTHGGGIHAEMTGQNVTECTGGAMAVTDENL 418 ********************************************************************* PP TIGR01358 412 asryetacdPrlnaeqslelaflvaeklre 441 a+ry+t+cdPrlna qslelafl+ae+l++ lcl|NCBI__GCF_000016765.1:WP_011951238.1 419 ADRYHTHCDPRLNAGQSLELAFLLAEMLNQ 448 ***************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (458 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: 12.33 // [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