Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate PP_1866 PP_1866 Phospho-2-dehydro-3-deoxyheptonate aldolase
Query= BRENDA::P29976 (525 letters) >FitnessBrowser__Putida:PP_1866 Length = 448 Score = 561 bits (1446), Expect = e-164 Identities = 271/444 (61%), Positives = 335/444 (75%), Gaps = 1/444 (0%) Query: 75 WTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKAFLL 134 W+P+SW+ Q P YP+A L V +T+ ++PP+VFAGEAR L + A+ G+AFLL Sbjct: 5 WSPDSWRALPIQQQPTYPDAAHLLKVEQTLASYPPLVFAGEARELRRQFAEVTEGRAFLL 64 Query: 135 QGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAFEEK 194 QGGDCAESF EF+A IRDTF+VLLQM+IV+TF PV+KVGRMAGQFAKPRS E Sbjct: 65 QGGDCAESFAEFSAAKIRDTFKVLLQMAIVMTFAAGCPVVKVGRMAGQFAKPRSSGDETI 124 Query: 195 DGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQRVTQ 254 V LP+Y+GD +NG FD KSRIPDP R+++AY Q+ A+LNLLRAFA GG+A + +V + Sbjct: 125 GDVTLPAYRGDIVNGIGFDAKSRIPDPERLLQAYHQATASLNLLRAFAQGGFADLHQVHK 184 Query: 255 WNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTDHPLMTTTDFYTSHECLLLPYEQS 314 WNLDF+ S AD+Y +LANR+DE L FM ACGL + P + T F+T+HE LLL YE++ Sbjct: 185 WNLDFIANSALADKYHQLANRIDETLAFMRACGLDSA-PQLRETSFFTAHEALLLNYEEA 243 Query: 315 LTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFELVKLV 374 R DS +G YYDCSAHM+W G+RTRQLDGAHVEFLRG+ NP+G+KV M+P EL++L+ Sbjct: 244 FVRQDSLTGDYYDCSAHMLWIGDRTRQLDGAHVEFLRGVHNPIGVKVGPSMNPEELIRLI 303 Query: 375 EILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAPCGLK 434 + LNP N PGR+ +IVRMGA + LP LIR V R G+ V W DPMHGNTIKA G K Sbjct: 304 DTLNPANDPGRLNLIVRMGAGKVGDHLPGLIRTVEREGRKVLWSSDPMHGNTIKASSGYK 363 Query: 435 TRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRYHTHC 494 TR F IL EV+ F VH+ EGSHAGGIH+EMTGQNVTECIGG+R +T D LS RYHTHC Sbjct: 364 TRDFAQILDEVKQFFQVHQAEGSHAGGIHIEMTGQNVTECIGGARPITEDALSDRYHTHC 423 Query: 495 DPRLNASQSLELAFIVAERLRKRR 518 DPR+NA QSLELAF++AE L++ R Sbjct: 424 DPRMNADQSLELAFLIAETLKQVR 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: 662 Number of extensions: 19 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: 448 Length adjustment: 34 Effective length of query: 491 Effective length of database: 414 Effective search space: 203274 Effective search space used: 203274 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 PP_1866 PP_1866 (Phospho-2-dehydro-3-deoxyheptonate aldolase)
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.12408.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-224 730.4 0.0 3.4e-224 730.2 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_1866 PP_1866 Phospho-2-dehydro-3-deox Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1866 PP_1866 Phospho-2-dehydro-3-deoxyheptonate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 730.2 0.0 3.4e-224 3.4e-224 1 443 [] 5 447 .. 5 447 .. 1.00 Alignments for each domain: == domain 1 score: 730.2 bits; conditional E-value: 3.4e-224 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkevead 75 ws++swr+ p +q+P+yPda++l +v++tl+s+PPlv+age+++l++++aev++G+afllqgGdcaesf e++a+ lcl|FitnessBrowser__Putida:PP_1866 5 WSPDSWRALPIQQQPTYPDAAHLLKVEQTLASYPPLVFAGEARELRRQFAEVTEGRAFLLQGGDCAESFAEFSAA 79 89************************************************************************* PP TIGR01358 76 nirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvpdperl 150 +ird+++vllqma+v+t++a+ Pvvkvgr+aGq+akPrs+ e+ ++vtlp+yrGd++ng fd+++r+pdperl lcl|FitnessBrowser__Putida:PP_1866 80 KIRDTFKVLLQMAIVMTFAAGCPVVKVGRMAGQFAKPRSSGDETIGDVTLPAYRGDIVNGIGFDAKSRIPDPERL 154 *************************************************************************** PP TIGR01358 151 vrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeaealkrvel 225 ++ay++++a+lnllra+++gG+adl++vh+Wnl+f+ +s +++y++la++ide+l fm+a+g+++a +l+++ + lcl|FitnessBrowser__Putida:PP_1866 155 LQAYHQATASLNLLRAFAQGGFADLHQVHKWNLDFIANSALADKYHQLANRIDETLAFMRACGLDSAPQLRETSF 229 *************************************************************************** PP TIGR01358 226 ytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgpsmeadellklie 300 +t+healll+yeea++r+ds +g+++d+sah+lWiG+rtrqldgahveflrgv+nPig+kvgpsm+++el++li+ lcl|FitnessBrowser__Putida:PP_1866 230 FTAHEALLLNYEEAFVRQDSLTGDYYDCSAHMLWIGDRTRQLDGAHVEFLRGVHNPIGVKVGPSMNPEELIRLID 304 *************************************************************************** PP TIGR01358 301 vldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrrfddilsevkeffe 375 l+P n+PGrl li+r+Ga k+ ++lP l++ v+++Gr+v+W +dpmhGnt++a+sGyktr f +il+evk+ff+ lcl|FitnessBrowser__Putida:PP_1866 305 TLNPANDPGRLNLIVRMGAGKVGDHLPGLIRTVEREGRKVLWSSDPMHGNTIKASSGYKTRDFAQILDEVKQFFQ 379 *************************************************************************** PP TIGR01358 376 vhkaeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflvaeklrear 443 vh+aeG+h GG+h+e+tG++vtec+GGar ite+ l++ry+t+cdPr+na+qslelafl+ae+l+++r lcl|FitnessBrowser__Putida:PP_1866 380 VHQAEGSHAGGIHIEMTGQNVTECIGGARPITEDALSDRYHTHCDPRMNADQSLELAFLIAETLKQVR 447 ****************************************************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (448 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: 7.20 // [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