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_012115203.1 XAUT_RS16230 3-deoxy-7-phosphoheptulonate synthase class II
Query= SwissProt::A0A067XGX8 (512 letters) >NCBI__GCF_000017645.1:WP_012115203.1 Length = 478 Score = 552 bits (1423), Expect = e-162 Identities = 270/465 (58%), Positives = 337/465 (72%), Gaps = 1/465 (0%) Query: 43 TKPRTKHISAVQSPPSTTKWNLESWKTKPAFQLPDYPDKVELESVLKTLSTYPPIVFAGE 102 T+P++ + ++ W +SW+ P Q+P+YPDK EL V L++YPP+VFAGE Sbjct: 3 TRPQSAPVPGAEASRRAEGWRPDSWRFYPGVQMPNYPDKAELAEVEAKLASYPPLVFAGE 62 Query: 103 ARNLEEKLGEAALGNAFLLQGGDCAESFKEFSANNIRDTFRVMLQMGVVLMFGGQMPVIK 162 AR L+ ++ + A G AFLLQGGDCAESF E SA+NIRD FRV LQM VVL F G PV+K Sbjct: 63 ARRLKAEIAKVARGEAFLLQGGDCAESFDEHSADNIRDFFRVFLQMAVVLTFAGGSPVVK 122 Query: 163 VGRMAGQFAKPRSDPFEEKDGVKLPSYRGDNVNGDAFDEKSRIPDPHRMVRAYTQSVATL 222 VGR+AGQFAKPRS E ++GV LPSYRGD VN AF E +R+PDP R + AY QS ATL Sbjct: 123 VGRIAGQFAKPRSSDTETENGVTLPSYRGDIVNDIAFTEAARVPDPRRQIEAYRQSAATL 182 Query: 223 NLLRAFASGGYAAMQRVNQWNLDFTDQSEQGDRYRELAHRVDEAMGFMTAAGLTVD-HTI 281 NLLRAFA+GGYA ++ +QW L F S Q RY+ELA+R+ EA+ FM A G+ H Sbjct: 183 NLLRAFANGGYANLENAHQWMLGFVKDSPQSSRYQELANRITEALDFMRACGINPQSHPE 242 Query: 282 MTTTDFWTSHECLLLPYEQALTREDSTSGLYYDCSAHMIWVGERTRQLDGAHVEFLRGIA 341 M TTDF+TSHE LLL YEQALTR DSTSG +Y S H++W+G+RTRQ D AHVE+ RGI Sbjct: 243 MRTTDFFTSHEALLLGYEQALTRVDSTSGDWYATSGHLLWIGDRTRQPDHAHVEYFRGIR 302 Query: 342 NPLGIKVSHKMDPDELVKLIDILNPQNKPGRITVITRMGADNMRVKLPHLIRAVRGAGQI 401 NP+GIK + D L++L+D+L P N+PGRIT+I R GAD + LP LIRAV G++ Sbjct: 303 NPIGIKCGPSITGDGLIRLLDMLQPDNEPGRITLICRFGADKVGDYLPGLIRAVEKEGRV 362 Query: 402 VTWVSDPMHGNTTKAPCGLKTRSFDSIRAELRAFFDVHEQEGSYPGGVHLEMTGQNVTEC 461 V W DPMHGNT KA G KTR F+ I++E+R+FFD+H EG++ GGVHLEMTG+NVTEC Sbjct: 363 VAWSCDPMHGNTIKAASGYKTRPFERIQSEIRSFFDIHAAEGTFAGGVHLEMTGKNVTEC 422 Query: 462 VGGSRTITYNDLSSRYHTHCDPRLNASQALELAFAIAERLRRRRL 506 GG+R I+ DL RYHT+CDPRLNA QA+E AF +AE L+R RL Sbjct: 423 TGGARAISDEDLRDRYHTYCDPRLNAEQAIETAFLVAELLKRERL 467 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: 697 Number of extensions: 24 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: 478 Length adjustment: 34 Effective length of query: 478 Effective length of database: 444 Effective search space: 212232 Effective search space used: 212232 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_012115203.1 XAUT_RS16230 (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.29869.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-220 717.1 0.0 3.7e-220 716.9 0.0 1.0 1 lcl|NCBI__GCF_000017645.1:WP_012115203.1 XAUT_RS16230 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017645.1:WP_012115203.1 XAUT_RS16230 3-deoxy-7-phosphoheptulonate synthase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 716.9 0.0 3.7e-220 3.7e-220 1 442 [. 22 465 .. 22 466 .. 0.99 Alignments for each domain: == domain 1 score: 716.9 bits; conditional E-value: 3.7e-220 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 w+++swr p +q+P+yPd+++l +v+++l+s+PPlv+age+++lk+++a+va+GeafllqgGdcaesf lcl|NCBI__GCF_000017645.1:WP_012115203.1 22 WRPDSWRFYPGVQMPNYPDKAELAEVEAKLASYPPLVFAGEARRLKAEIAKVARGEAFLLQGGDCAESF 90 89******************************************************************* PP TIGR01358 70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138 +e +adnird +rv+lqmavvlt++++ PvvkvgriaGq+akPrs+++e+++gvtlpsyrGd++n af lcl|NCBI__GCF_000017645.1:WP_012115203.1 91 DEHSADNIRDFFRVFLQMAVVLTFAGGSPVVKVGRIAGQFAKPRSSDTETENGVTLPSYRGDIVNDIAF 159 ********************************************************************* PP TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207 +eaarvpdp+r ++ay +saatlnllra+++gGya+l++ h+W l fvk+sp+++ry++la++i+eal lcl|NCBI__GCF_000017645.1:WP_012115203.1 160 TEAARVPDPRRQIEAYRQSAATLNLLRAFANGGYANLENAHQWMLGFVKDSPQSSRYQELANRITEALD 228 ********************************************************************* PP TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274 fm+a+g+++++ ++++++++tshealll ye+altrvds++g+++ +s+hllWiG+rtrq d+ahve+ lcl|NCBI__GCF_000017645.1:WP_012115203.1 229 FMRACGINPQShpEMRTTDFFTSHEALLLGYEQALTRVDSTSGDWYATSGHLLWIGDRTRQPDHAHVEY 297 ********998899******************************************************* PP TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343 rg++nPigik+gps+++d l++l+++l+P+nePGr+tli r+Ga+k+ + lP l++av+++Gr v+W lcl|NCBI__GCF_000017645.1:WP_012115203.1 298 FRGIRNPIGIKCGPSITGDGLIRLLDMLQPDNEPGRITLICRFGADKVGDYLPGLIRAVEKEGRVVAWS 366 ********************************************************************* PP TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412 +dpmhGnt++aasGyktr f++i+se+++ff++h+aeGt+ GGvhle+tG++vtec+GGar+i+++dl lcl|NCBI__GCF_000017645.1:WP_012115203.1 367 CDPMHGNTIKAASGYKTRPFERIQSEIRSFFDIHAAEGTFAGGVHLEMTGKNVTECTGGARAISDEDLR 435 ********************************************************************* PP TIGR01358 413 sryetacdPrlnaeqslelaflvaeklrea 442 +ry+t cdPrlnaeq++e aflvae l+ + lcl|NCBI__GCF_000017645.1:WP_012115203.1 436 DRYHTYCDPRLNAEQAIETAFLVAELLKRE 465 *************************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (478 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: 00:00:00.01 # Mc/sec: 11.32 // [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