Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_012331539.1 M446_RS07685 3-deoxy-7-phosphoheptulonate synthase class II
Query= BRENDA::P29976 (525 letters) >NCBI__GCF_000019365.1:WP_012331539.1 Length = 460 Score = 542 bits (1396), Expect = e-158 Identities = 261/451 (57%), Positives = 334/451 (74%), Gaps = 2/451 (0%) Query: 74 KWTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKAFL 133 +WTP SW+ Q+PDYP+A LE+V + + +FPP+VFAGEAR L+ LA A G+AFL Sbjct: 4 RWTPSSWRRLPIQQVPDYPDAVALEAVERQLASFPPLVFAGEARKLKRSLATVAAGEAFL 63 Query: 134 LQGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAFEE 193 LQGGDCAESF E +A NIRD FRV LQM++VLTF G PV+KVGR+AGQFAKPRS E Sbjct: 64 LQGGDCAESFDEHSADNIRDFFRVFLQMALVLTFAGGSPVVKVGRIAGQFAKPRSSPTET 123 Query: 194 KDGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQRVT 253 +DGV LPSY+GD +NG F + RIPDP R + AY QSAATLNLLRAFATGGYA ++ Sbjct: 124 QDGVALPSYRGDIVNGIGFTAEDRIPDPRRQVEAYRQSAATLNLLRAFATGGYANLENAH 183 Query: 254 QWNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTD-HPLMTTTDFYTSHECLLLPYE 312 +W L FV+ S Q+ Y++LA R+ E L FM A G+ + H + TDFYTSHE LLL YE Sbjct: 184 RWMLGFVKDSPQSSAYEDLAQRMTETLDFMRAIGINPETHQEVRQTDFYTSHEALLLGYE 243 Query: 313 QSLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFELVK 372 Q+LTR+DSTSG +Y S HM+W G+RTRQ D AH+E+ RGI NP+G+K + P +L++ Sbjct: 244 QALTRVDSTSGDWYATSGHMLWIGDRTRQADHAHIEYARGIKNPVGLKCGPSLKPDDLIR 303 Query: 373 LVEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAPCG 432 L+ +LNP N+PGR+T+I R GA+ + LP LIRAV R G+ V W CDPMHGNT+ A G Sbjct: 304 LIGLLNPENEPGRLTLICRFGADKVGDHLPGLIRAVEREGRKVVWSCDPMHGNTVTA-SG 362 Query: 433 LKTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRYHT 492 KTR F+ ++ E++ F DVH EG++AGGIHLEMTG+NVTEC GG+R +T DDL RYHT Sbjct: 363 FKTRPFERVMKEIQGFFDVHRAEGTYAGGIHLEMTGKNVTECTGGARALTADDLRDRYHT 422 Query: 493 HCDPRLNASQSLELAFIVAERLRKRRTGSQR 523 +CDPRLNA Q+LE+AF+ A+ +++ R +R Sbjct: 423 YCDPRLNAEQALEVAFLTADLVKRERRDKER 453 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: 644 Number of extensions: 26 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: 460 Length adjustment: 34 Effective length of query: 491 Effective length of database: 426 Effective search space: 209166 Effective search space used: 209166 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_012331539.1 M446_RS07685 (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.4280.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-216 703.9 0.0 3.7e-216 703.7 0.0 1.0 1 lcl|NCBI__GCF_000019365.1:WP_012331539.1 M446_RS07685 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019365.1:WP_012331539.1 M446_RS07685 3-deoxy-7-phosphoheptulonate synthase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 703.7 0.0 3.7e-216 3.7e-216 1 441 [. 5 446 .. 5 449 .. 0.99 Alignments for each domain: == domain 1 score: 703.7 bits; conditional E-value: 3.7e-216 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 w+++swr p +q+P+yPda aleav+ +l+s+PPlv+age++klk++la va+GeafllqgGdcaesf lcl|NCBI__GCF_000019365.1:WP_012331539.1 5 WTPSSWRRLPIQQVPDYPDAVALEAVERQLASFPPLVFAGEARKLKRSLATVAAGEAFLLQGGDCAESF 73 89******************************************************************* PP TIGR01358 70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138 +e +adnird +rv+lqma+vlt++++ PvvkvgriaGq+akPrs+p+e++dgv lpsyrGd++ng f lcl|NCBI__GCF_000019365.1:WP_012331539.1 74 DEHSADNIRDFFRVFLQMALVLTFAGGSPVVKVGRIAGQFAKPRSSPTETQDGVALPSYRGDIVNGIGF 142 ********************************************************************* PP TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207 ++++r+pdp+r v+ay +saatlnllra+++gGya+l++ h+W l fvk+sp+++ ye+la++++e+l lcl|NCBI__GCF_000019365.1:WP_012331539.1 143 TAEDRIPDPRRQVEAYRQSAATLNLLRAFATGGYANLENAHRWMLGFVKDSPQSSAYEDLAQRMTETLD 211 ********************************************************************* PP TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274 fm+a+g+++++ +++++++ytshealll ye+altrvds++g+++ +s+h+lWiG+rtrq d+ah+e+ lcl|NCBI__GCF_000019365.1:WP_012331539.1 212 FMRAIGINPEThqEVRQTDFYTSHEALLLGYEQALTRVDSTSGDWYATSGHMLWIGDRTRQADHAHIEY 280 *******9887779******************************************************* PP TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343 +rg+knP+g+k+gps+++d+l++li l+PenePGrltli r+Ga+k+ ++lP l++av+++Gr+vvW lcl|NCBI__GCF_000019365.1:WP_012331539.1 281 ARGIKNPVGLKCGPSLKPDDLIRLIGLLNPENEPGRLTLICRFGADKVGDHLPGLIRAVEREGRKVVWS 349 ********************************************************************* PP TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412 +dpmhGnt++ asG+ktr f+++++e+++ff+vh+aeGt+ GG+hle+tG++vtec+GGar++t +dl lcl|NCBI__GCF_000019365.1:WP_012331539.1 350 CDPMHGNTVT-ASGFKTRPFERVMKEIQGFFDVHRAEGTYAGGIHLEMTGKNVTECTGGARALTADDLR 417 ********75.68******************************************************** PP TIGR01358 413 sryetacdPrlnaeqslelaflvaeklre 441 +ry+t cdPrlnaeq+le+afl a+ ++ lcl|NCBI__GCF_000019365.1:WP_012331539.1 418 DRYHTYCDPRLNAEQALEVAFLTADLVKR 446 ***********************998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (460 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: 00:00:00.02 # Mc/sec: 9.47 // [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