Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_014597024.1 PST_RS12605 3-deoxy-7-phosphoheptulonate synthase class II
Query= BRENDA::P29976 (525 letters) >NCBI__GCF_000013785.1:WP_014597024.1 Length = 449 Score = 563 bits (1451), Expect = e-165 Identities = 270/444 (60%), Positives = 336/444 (75%), Gaps = 1/444 (0%) Query: 75 WTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKAFLL 134 W+P+SW+ K Q P+YP+A L+ V +T+ PP+VFAGEAR L + A+ G+AFLL Sbjct: 5 WSPDSWRNKPIQQQPEYPDAEHLKRVERTLAGLPPLVFAGEARELRRQFAEVTRGRAFLL 64 Query: 135 QGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAFEEK 194 QGGDCAESF EF+AT IRDTF+VLLQM+IV+TF PV+KVGRMAGQFAKPRS E Sbjct: 65 QGGDCAESFAEFSATKIRDTFKVLLQMAIVMTFAAGCPVVKVGRMAGQFAKPRSAGDETI 124 Query: 195 DGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQRVTQ 254 DGV LP+Y+GD +NG F+ KSR+PDP R+++AY QS A+LNLLRAFA GG+A + +V Q Sbjct: 125 DGVTLPAYRGDIVNGIDFNAKSRVPDPERLLQAYHQSTASLNLLRAFAQGGFADLHQVHQ 184 Query: 255 WNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTDHPLMTTTDFYTSHECLLLPYEQS 314 WNLDF+ S A++Y +L R+DE L FM ACGL P + T F+T+HE LLL YEQ+ Sbjct: 185 WNLDFIANSLLAEKYHQLGARIDETLKFMRACGLD-GAPQLRETSFFTAHEALLLNYEQA 243 Query: 315 LTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFELVKLV 374 R DS SG +YDCSAHM+W G+RTRQLDGAHVEFLRG+ NP+G+KV M EL++L+ Sbjct: 244 FVRQDSLSGGWYDCSAHMLWIGDRTRQLDGAHVEFLRGVGNPIGVKVGPSMATDELIRLI 303 Query: 375 EILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAPCGLK 434 +ILNP N PGR+ +IVRMGA+ + LP L+RAV+ G+ V W DPMHGNT+KA G K Sbjct: 304 DILNPQNDPGRLNLIVRMGADKVEAGLPRLVRAVQNEGRQVLWSSDPMHGNTMKASSGYK 363 Query: 435 TRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRYHTHC 494 TR F+ +LAEVR F DVH EGS+ GGIH+EMTGQNVTECIGGSR +T L RYHTHC Sbjct: 364 TRDFERVLAEVRQFFDVHRAEGSYPGGIHIEMTGQNVTECIGGSRPITEAGLCDRYHTHC 423 Query: 495 DPRLNASQSLELAFIVAERLRKRR 518 DPRLNA QSLE+AF++AE L++ R Sbjct: 424 DPRLNADQSLEMAFMIAETLKQVR 447 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: 627 Number of extensions: 17 Number of successful extensions: 2 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: 449 Length adjustment: 34 Effective length of query: 491 Effective length of database: 415 Effective search space: 203765 Effective search space used: 203765 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_014597024.1 PST_RS12605 (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.15471.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-225 733.2 0.0 4.8e-225 733.0 0.0 1.0 1 lcl|NCBI__GCF_000013785.1:WP_014597024.1 PST_RS12605 3-deoxy-7-phosphohep Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013785.1:WP_014597024.1 PST_RS12605 3-deoxy-7-phosphoheptulonate synthase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 733.0 0.0 4.8e-225 4.8e-225 1 443 [] 5 447 .. 5 447 .. 1.00 Alignments for each domain: == domain 1 score: 733.0 bits; conditional E-value: 4.8e-225 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 ws++swr+kp +q+PeyPdae+l++v+ tl+ lPPlv+age+++l++++aev++G+afllqgGdcaesf lcl|NCBI__GCF_000013785.1:WP_014597024.1 5 WSPDSWRNKPIQQQPEYPDAEHLKRVERTLAGLPPLVFAGEARELRRQFAEVTRGRAFLLQGGDCAESF 73 89******************************************************************* PP TIGR01358 70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138 e++a +ird+++vllqma+v+t++a+ Pvvkvgr+aGq+akPrs+ e+ dgvtlp+yrGd++ng +f lcl|NCBI__GCF_000013785.1:WP_014597024.1 74 AEFSATKIRDTFKVLLQMAIVMTFAAGCPVVKVGRMAGQFAKPRSAGDETIDGVTLPAYRGDIVNGIDF 142 ********************************************************************* PP TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207 ++++rvpdperl++ay++s+a+lnllra+++gG+adl++vh+Wnl+f+ +s +++y++l +ide+l+ lcl|NCBI__GCF_000013785.1:WP_014597024.1 143 NAKSRVPDPERLLQAYHQSTASLNLLRAFAQGGFADLHQVHQWNLDFIANSLLAEKYHQLGARIDETLK 211 ********************************************************************* PP TIGR01358 208 fmsavgvaeaealkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflr 276 fm+a+g++ a +l+++ ++t+healll+ye+a++r+ds +g+++d+sah+lWiG+rtrqldgahveflr lcl|NCBI__GCF_000013785.1:WP_014597024.1 212 FMRACGLDGAPQLRETSFFTAHEALLLNYEQAFVRQDSLSGGWYDCSAHMLWIGDRTRQLDGAHVEFLR 280 ********************************************************************* PP TIGR01358 277 gvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtd 345 gv nPig+kvgpsm +del++li++l+P+n+PGrl li+r+Ga+k+ lP+l++av+++Gr+v+W +d lcl|NCBI__GCF_000013785.1:WP_014597024.1 281 GVGNPIGVKVGPSMATDELIRLIDILNPQNDPGRLNLIVRMGADKVEAGLPRLVRAVQNEGRQVLWSSD 349 ********************************************************************* PP TIGR01358 346 pmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasr 414 pmhGnt++a+sGyktr f+++l+ev++ff+vh+aeG++pGG+h+e+tG++vtec+GG+r ite l +r lcl|NCBI__GCF_000013785.1:WP_014597024.1 350 PMHGNTMKASSGYKTRDFERVLAEVRQFFDVHRAEGSYPGGIHIEMTGQNVTECIGGSRPITEAGLCDR 418 ********************************************************************* PP TIGR01358 415 yetacdPrlnaeqslelaflvaeklrear 443 y+t+cdPrlna+qsle+af++ae+l+++r lcl|NCBI__GCF_000013785.1:WP_014597024.1 419 YHTHCDPRLNADQSLEMAFMIAETLKQVR 447 *************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (449 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.58 // [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