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_020175240.1 A3OQ_RS0109975 3-deoxy-7-phosphoheptulonate synthase class II
Query= SwissProt::A0A067XGX8 (512 letters) >NCBI__GCF_000385335.1:WP_020175240.1 Length = 462 Score = 532 bits (1370), Expect = e-155 Identities = 262/450 (58%), Positives = 325/450 (72%), Gaps = 1/450 (0%) Query: 58 STTKWNLESWKTKPAFQLPDYPDKVELESVLKTLSTYPPIVFAGEARNLEEKLGEAALGN 117 S +W +SW+ KP Q+PDYPD V L+ V + L+ +PP+VFAGEAR L++ L + A G Sbjct: 2 SVERWAPDSWRAKPIEQVPDYPDAVVLDEVERQLAGFPPLVFAGEARKLKKYLAKVAQGE 61 Query: 118 AFLLQGGDCAESFKEFSANNIRDTFRVMLQMGVVLMFGGQMPVIKVGRMAGQFAKPRSDP 177 AFLLQGGDCAESF E +A+NIRD FRV LQM VV+ F PV+KVGR+AGQFAKPRS P Sbjct: 62 AFLLQGGDCAESFDEHAADNIRDFFRVFLQMAVVMTFAAASPVVKVGRIAGQFAKPRSAP 121 Query: 178 FEEKDGVKLPSYRGDNVNGDAFDEKSRIPDPHRMVRAYTQSVATLNLLRAFASGGYAAMQ 237 E+ V+LPSYRGD VN AFDE +RIPDP R + AY QS ATLNLLRAFASGGYA ++ Sbjct: 122 NEKIGDVELPSYRGDIVNDIAFDEAARIPDPRRQLMAYRQSAATLNLLRAFASGGYANLE 181 Query: 238 RVNQWNLDFTDQSEQGDRYRELAHRVDEAMGFMTAAGLTVD-HTIMTTTDFWTSHECLLL 296 ++W L F + Q RY ELA R+ E +GFM A GL + H + T+F+TSHE LLL Sbjct: 182 NAHRWMLGFIKDTPQSARYSELADRLTETIGFMRAIGLDPETHQELRQTEFYTSHEALLL 241 Query: 297 PYEQALTREDSTSGLYYDCSAHMIWVGERTRQLDGAHVEFLRGIANPLGIKVSHKMDPDE 356 YEQALTR DST+G YY S HMIWVG+RTR AH+E+ RG+ NP+G+K M PD+ Sbjct: 242 GYEQALTRVDSTTGDYYATSGHMIWVGDRTRDPGHAHIEYARGVKNPIGLKCGPSMKPDD 301 Query: 357 LVKLIDILNPQNKPGRITVITRMGADNMRVKLPHLIRAVRGAGQIVTWVSDPMHGNTTKA 416 L++L DIL+P N+ GR+T+I R G D + L L+RA++ G+ V W DPMHGNT KA Sbjct: 302 LLRLADILDPANEAGRLTLICRFGTDKVAEHLVPLVRAIKKEGRTVVWSCDPMHGNTVKA 361 Query: 417 PCGLKTRSFDSIRAELRAFFDVHEQEGSYPGGVHLEMTGQNVTECVGGSRTITYNDLSSR 476 G KTR FD I E+R+FF VH+ EG+Y GGVHLEMTG+NVTEC GG+R IT DL R Sbjct: 362 GSGFKTRPFDRIMGEIRSFFAVHQAEGTYAGGVHLEMTGKNVTECTGGARAITEADLHDR 421 Query: 477 YHTHCDPRLNASQALELAFAIAERLRRRRL 506 YHTHCDPRLNA Q++E+AF +AE L+ R+ Sbjct: 422 YHTHCDPRLNAEQSIEVAFLVAELLKAERI 451 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: 709 Number of extensions: 26 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: 512 Length of database: 462 Length adjustment: 34 Effective length of query: 478 Effective length of database: 428 Effective search space: 204584 Effective search space used: 204584 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_020175240.1 A3OQ_RS0109975 (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.27472.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-215 699.9 0.0 6.3e-215 699.7 0.0 1.0 1 lcl|NCBI__GCF_000385335.1:WP_020175240.1 A3OQ_RS0109975 3-deoxy-7-phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000385335.1:WP_020175240.1 A3OQ_RS0109975 3-deoxy-7-phosphoheptulonate synthase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 699.7 0.0 6.3e-215 6.3e-215 1 442 [. 6 449 .. 6 450 .. 0.99 Alignments for each domain: == domain 1 score: 699.7 bits; conditional E-value: 6.3e-215 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 w+++swr+kp q+P+yPda l++v+ +l+ +PPlv+age++klk+ la+va+GeafllqgGdcaesf lcl|NCBI__GCF_000385335.1:WP_020175240.1 6 WAPDSWRAKPIEQVPDYPDAVVLDEVERQLAGFPPLVFAGEARKLKKYLAKVAQGEAFLLQGGDCAESF 74 89******************************************************************* PP TIGR01358 70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138 +e adnird +rv+lqmavv+t++a PvvkvgriaGq+akPrs+p e+ ++v+lpsyrGd++n af lcl|NCBI__GCF_000385335.1:WP_020175240.1 75 DEHAADNIRDFFRVFLQMAVVMTFAAASPVVKVGRIAGQFAKPRSAPNEKIGDVELPSYRGDIVNDIAF 143 ********************************************************************* PP TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207 deaar+pdp+r + ay +saatlnllra++sgGya+l++ h+W l f+k++p++ary +la++++e++ lcl|NCBI__GCF_000385335.1:WP_020175240.1 144 DEAARIPDPRRQLMAYRQSAATLNLLRAFASGGYANLENAHRWMLGFIKDTPQSARYSELADRLTETIG 212 ********************************************************************* PP TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274 fm+a+g+++++ +l+++e+ytshealll ye+altrvds++g+++ +s+h++W+G+rtr +ah+e+ lcl|NCBI__GCF_000385335.1:WP_020175240.1 213 FMRAIGLDPEThqELRQTEFYTSHEALLLGYEQALTRVDSTTGDYYATSGHMIWVGDRTRDPGHAHIEY 281 ********988789******************************************************* PP TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343 +rgvknPig+k+gpsm++d+ll+l ++ldP ne Grltli r+G++k+ae+l +l++a+k++Gr+vvW lcl|NCBI__GCF_000385335.1:WP_020175240.1 282 ARGVKNPIGLKCGPSMKPDDLLRLADILDPANEAGRLTLICRFGTDKVAEHLVPLVRAIKKEGRTVVWS 350 ********************************************************************* PP TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412 +dpmhGnt++a+sG+ktr fd+i+ e+++ff+vh+aeGt+ GGvhle+tG++vtec+GGar+ite dl+ lcl|NCBI__GCF_000385335.1:WP_020175240.1 351 CDPMHGNTVKAGSGFKTRPFDRIMGEIRSFFAVHQAEGTYAGGVHLEMTGKNVTECTGGARAITEADLH 419 ********************************************************************* PP TIGR01358 413 sryetacdPrlnaeqslelaflvaeklrea 442 +ry+t+cdPrlnaeqs+e+aflvae l+++ lcl|NCBI__GCF_000385335.1:WP_020175240.1 420 DRYHTHCDPRLNAEQSIEVAFLVAELLKAE 449 **************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (462 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: 7.33 // [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