Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate GFF1762 Psest_1801 3-deoxy-7-phosphoheptulonate synthase, class II
Query= BRENDA::P29976 (525 letters) >FitnessBrowser__psRCH2:GFF1762 Length = 449 Score = 565 bits (1456), 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 WSPDSWRSKPIQQQPEYPDAEHLSRVERTLAGLPPLVFAGEARELRRQFAEVTQGRAFLL 64 Query: 135 QGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAFEEK 194 QGGDCAESF EF+AT IRDTF+VLLQM+IV+TF PV+KVGRMAGQFAKPRS E Sbjct: 65 QGGDCAESFAEFSATKIRDTFKVLLQMAIVMTFAAGCPVVKVGRMAGQFAKPRSAGDETV 124 Query: 195 DGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQRVTQ 254 DGV LP+Y+GD +NG F+ +SR+PDP R+++AY QS ++LNLLRAFA GG+A + +V Q Sbjct: 125 DGVTLPAYRGDIVNGIDFNAQSRVPDPERLLQAYHQSTSSLNLLRAFAQGGFADLHQVHQ 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 MD EL++L+ Sbjct: 244 FVRQDSLSGGWYDCSAHMLWIGDRTRQLDGAHVEFLRGVGNPIGVKVGPSMDSEELIRLI 303 Query: 375 EILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAPCGLK 434 +ILNP N PGR+ +IVRMGA+ + LP L+RAV+ G+ V W DPMHGNTIKA G K Sbjct: 304 DILNPQNDPGRLNLIVRMGADKVEAGLPRLVRAVQNEGRHVLWSSDPMHGNTIKASSGYK 363 Query: 435 TRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRYHTHC 494 TR F+ +LAEVR F DVH EGS+ GGIH+EMTGQNVTECIGGSR +T LS RYHT C Sbjct: 364 TRDFEKVLAEVRQFFDVHRAEGSYPGGIHIEMTGQNVTECIGGSRPITEAGLSDRYHTQC 423 Query: 495 DPRLNASQSLELAFIVAERLRKRR 518 DPRLNA QSLE+AF++AE L++ R Sbjct: 424 DPRLNADQSLEMAFMIAETLKQLR 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: 624 Number of extensions: 15 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 GFF1762 Psest_1801 (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.23824.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-224 731.0 0.0 2.3e-224 730.8 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF1762 Psest_1801 3-deoxy-7-phosphohept Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1762 Psest_1801 3-deoxy-7-phosphoheptulonate synthase, class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 730.8 0.0 2.3e-224 2.3e-224 1 442 [. 5 446 .. 5 447 .. 1.00 Alignments for each domain: == domain 1 score: 730.8 bits; conditional E-value: 2.3e-224 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkevead 75 ws++swrskp +q+PeyPdae+l++v+ tl+ lPPlv+age+++l++++aev++G+afllqgGdcaesf e++a lcl|FitnessBrowser__psRCH2:GFF1762 5 WSPDSWRSKPIQQQPEYPDAEHLSRVERTLAGLPPLVFAGEARELRRQFAEVTQGRAFLLQGGDCAESFAEFSAT 79 89************************************************************************* PP TIGR01358 76 nirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvpdperl 150 +ird+++vllqma+v+t++a+ Pvvkvgr+aGq+akPrs+ e+ dgvtlp+yrGd++ng +f++++rvpdperl lcl|FitnessBrowser__psRCH2:GFF1762 80 KIRDTFKVLLQMAIVMTFAAGCPVVKVGRMAGQFAKPRSAGDETVDGVTLPAYRGDIVNGIDFNAQSRVPDPERL 154 *************************************************************************** PP TIGR01358 151 vrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeaealkrvel 225 ++ay++s+++lnllra+++gG+adl++vh+Wnl+f+ +s +++y++l +ide+l+fm+a+g++ a +l+++ + lcl|FitnessBrowser__psRCH2:GFF1762 155 LQAYHQSTSSLNLLRAFAQGGFADLHQVHQWNLDFIANSLLAEKYHQLGARIDETLKFMRACGLDGAPQLRETSF 229 *************************************************************************** PP TIGR01358 226 ytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgpsmeadellklie 300 +t+healll+ye+a++r+ds +g+++d+sah+lWiG+rtrqldgahveflrgv nPig+kvgpsm ++el++li+ lcl|FitnessBrowser__psRCH2:GFF1762 230 FTAHEALLLNYEQAFVRQDSLSGGWYDCSAHMLWIGDRTRQLDGAHVEFLRGVGNPIGVKVGPSMDSEELIRLID 304 *************************************************************************** PP TIGR01358 301 vldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrrfddilsevkeffe 375 +l+P+n+PGrl li+r+Ga+k+ lP+l++av+++Gr+v+W +dpmhGnt++a+sGyktr f+++l+ev++ff+ lcl|FitnessBrowser__psRCH2:GFF1762 305 ILNPQNDPGRLNLIVRMGADKVEAGLPRLVRAVQNEGRHVLWSSDPMHGNTIKASSGYKTRDFEKVLAEVRQFFD 379 *************************************************************************** PP TIGR01358 376 vhkaeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflvaeklrea 442 vh+aeG++pGG+h+e+tG++vtec+GG+r ite l++ry+t+cdPrlna+qsle+af++ae+l++ lcl|FitnessBrowser__psRCH2:GFF1762 380 VHRAEGSYPGGIHIEMTGQNVTECIGGSRPITEAGLSDRYHTQCDPRLNADQSLEMAFMIAETLKQL 446 ****************************************************************986 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: 7.37 // [ok]
This GapMind analysis is from Apr 09 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