Align Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic; 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2; DAHP synthase 2; PhDAHP2; Phospho-2-keto-3-deoxyheptonate aldolase 2; EC 2.5.1.54 (characterized)
to candidate WP_090217168.1 CV091_RS03245 3-deoxy-7-phosphoheptulonate synthase class II
Query= SwissProt::A0A067XGX8 (512 letters) >NCBI__GCF_002796795.1:WP_090217168.1 Length = 456 Score = 527 bits (1357), Expect = e-154 Identities = 260/448 (58%), Positives = 333/448 (74%), Gaps = 4/448 (0%) Query: 60 TKWNLESWKTKPAFQLPDYPDKVELESVLKTLSTYPPIVFAGEARNLEEKLGEAALGNAF 119 T W +W+ KP Q+PDY D L +V LS YPP+VFAGEAR L+++LG A G AF Sbjct: 2 TTWQKTNWRNKPRIQMPDYTDADALNAVEAQLSKYPPLVFAGEARRLKQQLGAAGRGEAF 61 Query: 120 LLQGGDCAESFKEFSANNIRDTFRVMLQMGVVLMFGGQMPVIKVGRMAGQFAKPRSDPFE 179 LLQGGDCAESF +FSA+ IRDTF+VMLQM +VL +G ++PV+KVGRMAGQFAKPRS P E Sbjct: 62 LLQGGDCAESFDQFSADAIRDTFKVMLQMAMVLTYGAKVPVVKVGRMAGQFAKPRSAPTE 121 Query: 180 EKDGVKLPSYRGDNVNGDAFDEKSRIPDPHRMVRAYTQSVATLNLLRAFASGGYAAMQRV 239 DG++LPSYRGD +N AF ++RIP+P +M++AYTQ+ ATLNLLRAF++GGYA + +V Sbjct: 122 TIDGLELPSYRGDIINDLAFTPEARIPNPQKMLQAYTQAAATLNLLRAFSTGGYADINQV 181 Query: 240 NQWNLDFTDQSEQGDRYRELAHRVDEAMGFMTAAGLTVD--HTIMTTTDFWTSHECLLLP 297 + W L FT+ SE+ D YR++A+R+ + + FM AAG+ D HT+ + DF+TSHE LLL Sbjct: 182 HAWTLGFTE-SEKVDAYRDMANRITDTLDFMNAAGVNKDTAHTLHSV-DFYTSHEGLLLE 239 Query: 298 YEQALTREDSTSGLYYDCSAHMIWVGERTRQLDGAHVEFLRGIANPLGIKVSHKMDPDEL 357 YE+ALTREDSTSG + S HMIW+G+RTRQ DGAHVEF G+ NP+G+K ++L Sbjct: 240 YEEALTREDSTSGDWLAGSGHMIWIGDRTRQPDGAHVEFCSGVLNPIGLKCGPTTTAEDL 299 Query: 358 VKLIDILNPQNKPGRITVITRMGADNMRVKLPHLIRAVRGAGQIVTWVSDPMHGNTTKAP 417 L+ LNP+N+ GR+T+I R GA LP L++AV+ G VTWV DPMHGNT K+ Sbjct: 300 KVLMKKLNPENEEGRLTLIARFGAGKAAEHLPRLVQAVKEEGATVTWVCDPMHGNTIKSS 359 Query: 418 CGLKTRSFDSIRAELRAFFDVHEQEGSYPGGVHLEMTGQNVTECVGGSRTITYNDLSSRY 477 G KTR F+++ E+R FF+VH EG+ PGGVH EMTGQ+VTEC GG R +T DLS+RY Sbjct: 360 TGYKTRPFENVLREVRDFFEVHNAEGTVPGGVHFEMTGQDVTECTGGIRAVTDEDLSARY 419 Query: 478 HTHCDPRLNASQALELAFAIAERLRRRR 505 HT CDPRLNASQ+LELAF +AE L +R Sbjct: 420 HTACDPRLNASQSLELAFLVAEELSNQR 447 Lambda K H 0.319 0.134 0.401 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: 658 Number of extensions: 20 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: 512 Length of database: 456 Length adjustment: 34 Effective length of query: 478 Effective length of database: 422 Effective search space: 201716 Effective search space used: 201716 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
Align candidate WP_090217168.1 CV091_RS03245 (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.2359771.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-212 691.4 0.0 2.5e-212 691.1 0.0 1.0 1 NCBI__GCF_002796795.1:WP_090217168.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002796795.1:WP_090217168.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 691.1 0.0 2.5e-212 2.5e-212 1 442 [. 4 446 .. 4 447 .. 0.99 Alignments for each domain: == domain 1 score: 691.1 bits; conditional E-value: 2.5e-212 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkeve 73 w++ wr+kp q+P+y da+al+av+++l+++PPlv+age+++lk++l+++ +GeafllqgGdcaesf++++ NCBI__GCF_002796795.1:WP_090217168.1 4 WQKTNWRNKPRIQMPDYTDADALNAVEAQLSKYPPLVFAGEARRLKQQLGAAGRGEAFLLQGGDCAESFDQFS 76 77899******************************************************************** PP TIGR01358 74 adnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvpd 146 ad ird+++v+lqma+vltyga++Pvvkvgr+aGq+akPrs+p+e+ dg++lpsyrGd+in af+ +ar+p+ NCBI__GCF_002796795.1:WP_090217168.1 77 ADAIRDTFKVMLQMAMVLTYGAKVPVVKVGRMAGQFAKPRSAPTETIDGLELPSYRGDIINDLAFTPEARIPN 149 ************************************************************************* PP TIGR01358 147 perlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeae. 218 p+++++ay+++aatlnllra+ +gGyad+++vh+W+l f+ +s++ + y+++a++i+++l fm+a+gv++++ NCBI__GCF_002796795.1:WP_090217168.1 150 PQKMLQAYTQAAATLNLLRAFSTGGYADINQVHAWTLGFT-ESEKVDAYRDMANRITDTLDFMNAAGVNKDTa 221 ***************************************8.58999*********************988776 PP TIGR01358 219 .alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgpsm 290 +l+ v++ytshe lll+yeealtr+ds++g++ s+h++WiG+rtrq dgahvef +gv nPig+k+gp++ NCBI__GCF_002796795.1:WP_090217168.1 222 hTLHSVDFYTSHEGLLLEYEEALTREDSTSGDWLAGSGHMIWIGDRTRQPDGAHVEFCSGVLNPIGLKCGPTT 294 69*********************************************************************** PP TIGR01358 291 eadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrrf 363 +a++l l+++l+Pene Grltli+r+Ga k ae+lP+l++avk++G++v+Wv+dpmhGnt+++++Gyktr f NCBI__GCF_002796795.1:WP_090217168.1 295 TAEDLKVLMKKLNPENEEGRLTLIARFGAGKAAEHLPRLVQAVKEEGATVTWVCDPMHGNTIKSSTGYKTRPF 367 ************************************************************************* PP TIGR01358 364 ddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflva 436 +++l ev+ ffevh+aeGt pGGvh e+tG+dvtec+GG r++t++dl+ ry+tacdPrlna+qslelaflva NCBI__GCF_002796795.1:WP_090217168.1 368 ENVLREVRDFFEVHNAEGTVPGGVHFEMTGQDVTECTGGIRAVTDEDLSARYHTACDPRLNASQSLELAFLVA 440 ************************************************************************* PP TIGR01358 437 eklrea 442 e l ++ NCBI__GCF_002796795.1:WP_090217168.1 441 EELSNQ 446 *99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (456 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 20.47 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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