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_013419234.1 RVAN_RS07975 3-deoxy-7-phosphoheptulonate synthase class II
Query= SwissProt::A0A067XGX8 (512 letters) >NCBI__GCF_000166055.1:WP_013419234.1 Length = 463 Score = 560 bits (1442), Expect = e-164 Identities = 271/449 (60%), Positives = 340/449 (75%), Gaps = 1/449 (0%) Query: 58 STTKWNLESWKTKPAFQLPDYPDKVELESVLKTLSTYPPIVFAGEARNLEEKLGEAALGN 117 S+ +W ESW++KP Q+P YPD+ EL +V K L+++PP+VFAGEAR L++ L E A G Sbjct: 2 SSPRWTPESWRSKPVEQVPVYPDEAELVAVEKELASFPPLVFAGEARGLQKGLAEVAHGR 61 Query: 118 AFLLQGGDCAESFKEFSANNIRDTFRVMLQMGVVLMFGGQMPVIKVGRMAGQFAKPRSDP 177 FLLQGGDCAESF E A++IRD FRV LQM VVL + G PV+KVGR+AGQFAKPRS P Sbjct: 62 GFLLQGGDCAESFSEHGADSIRDFFRVFLQMAVVLTYAGSRPVVKVGRIAGQFAKPRSAP 121 Query: 178 FEEKDGVKLPSYRGDNVNGDAFDEKSRIPDPHRMVRAYTQSVATLNLLRAFASGGYAAMQ 237 E+ V+LPSYRGD +N AF +SR PDP R+++AY QS ATLNLLRAFA GGYA ++ Sbjct: 122 TEKHGDVELPSYRGDIINDIAFSPESRTPDPRRLLKAYRQSAATLNLLRAFAQGGYADLE 181 Query: 238 RVNQWNLDFTDQSEQGDRYRELAHRVDEAMGFMTAAGLTVDHTI-MTTTDFWTSHECLLL 296 RV+QW L F S G+RY ELA+R+ + + FM A G+T D++ + TTDF+TSHE LLL Sbjct: 182 RVHQWTLGFVKDSPAGERYEELANRISDTLHFMRACGVTSDNSERLRTTDFYTSHEALLL 241 Query: 297 PYEQALTREDSTSGLYYDCSAHMIWVGERTRQLDGAHVEFLRGIANPLGIKVSHKMDPDE 356 YE+A R DSTSG +Y S H +W+G+RTRQLD AHVEFLRGI NP+G+K+ M PDE Sbjct: 242 GYEEAFARVDSTSGNWYATSGHFLWIGDRTRQLDHAHVEFLRGIRNPIGVKIGPSMKPDE 301 Query: 357 LVKLIDILNPQNKPGRITVITRMGADNMRVKLPHLIRAVRGAGQIVTWVSDPMHGNTTKA 416 L+ LIDILNP N+PGR+T+I R GAD + LP LIRAV+ G+IV W DPMHGNT K+ Sbjct: 302 LIDLIDILNPTNEPGRLTLIGRFGADKVGKYLPELIRAVKSEGKIVIWSCDPMHGNTIKS 361 Query: 417 PCGLKTRSFDSIRAELRAFFDVHEQEGSYPGGVHLEMTGQNVTECVGGSRTITYNDLSSR 476 G KTR F+ + AE+ FFD+ + EG YPGG+H+EMTG++VTEC GG+ +I+ DLS+R Sbjct: 362 ASGYKTRPFNQVLAEVETFFDICQAEGVYPGGLHVEMTGKDVTECTGGAHSISDADLSNR 421 Query: 477 YHTHCDPRLNASQALELAFAIAERLRRRR 505 YHT+CDPRLNA QALELAF +AERLRR R Sbjct: 422 YHTYCDPRLNADQALELAFLVAERLRRDR 450 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: 723 Number of extensions: 29 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: 463 Length adjustment: 34 Effective length of query: 478 Effective length of database: 429 Effective search space: 205062 Effective search space used: 205062 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_013419234.1 RVAN_RS07975 (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.32341.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-223 726.8 0.0 4.3e-223 726.6 0.0 1.0 1 lcl|NCBI__GCF_000166055.1:WP_013419234.1 RVAN_RS07975 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000166055.1:WP_013419234.1 RVAN_RS07975 3-deoxy-7-phosphoheptulonate synthase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 726.6 0.0 4.3e-223 4.3e-223 1 442 [. 6 449 .. 6 450 .. 0.99 Alignments for each domain: == domain 1 score: 726.6 bits; conditional E-value: 4.3e-223 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 w++eswrskp q+P yPd+++l av+++l+s+PPlv+age++ l++ laeva+G++fllqgGdcaesf lcl|NCBI__GCF_000166055.1:WP_013419234.1 6 WTPESWRSKPVEQVPVYPDEAELVAVEKELASFPPLVFAGEARGLQKGLAEVAHGRGFLLQGGDCAESF 74 89******************************************************************* PP TIGR01358 70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138 +e ad+ird +rv+lqmavvlty++s PvvkvgriaGq+akPrs+p+e++++v+lpsyrGd+in af lcl|NCBI__GCF_000166055.1:WP_013419234.1 75 SEHGADSIRDFFRVFLQMAVVLTYAGSRPVVKVGRIAGQFAKPRSAPTEKHGDVELPSYRGDIINDIAF 143 ********************************************************************* PP TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207 + ++r+pdp+rl++ay +saatlnllra+++gGyadl++vh+W+l fvk+spag+rye+la++i+++l+ lcl|NCBI__GCF_000166055.1:WP_013419234.1 144 SPESRTPDPRRLLKAYRQSAATLNLLRAFAQGGYADLERVHQWTLGFVKDSPAGERYEELANRISDTLH 212 ********************************************************************* PP TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274 fm+a+gv++++ l+++++ytshealll yeea+ rvds++g+++ +s+h+lWiG+rtrqld+ahvef lcl|NCBI__GCF_000166055.1:WP_013419234.1 213 FMRACGVTSDNseRLRTTDFYTSHEALLLGYEEAFARVDSTSGNWYATSGHFLWIGDRTRQLDHAHVEF 281 *******9988789******************************************************* PP TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343 lrg++nPig+k+gpsm++del+ li++l+P nePGrltli r+Ga+k+ + lPel++avk++G+ v+W lcl|NCBI__GCF_000166055.1:WP_013419234.1 282 LRGIRNPIGVKIGPSMKPDELIDLIDILNPTNEPGRLTLIGRFGADKVGKYLPELIRAVKSEGKIVIWS 350 ********************************************************************* PP TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412 +dpmhGnt+++asGyktr f+++l+ev++ff++ +aeG++pGG+h+e+tG+dvtec+GGa++i++ dl+ lcl|NCBI__GCF_000166055.1:WP_013419234.1 351 CDPMHGNTIKSASGYKTRPFNQVLAEVETFFDICQAEGVYPGGLHVEMTGKDVTECTGGAHSISDADLS 419 ********************************************************************* PP TIGR01358 413 sryetacdPrlnaeqslelaflvaeklrea 442 +ry+t cdPrlna+q+lelaflvae+lr lcl|NCBI__GCF_000166055.1:WP_013419234.1 420 NRYHTYCDPRLNADQALELAFLVAERLRRD 449 **************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (463 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: 7.97 // [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