Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_036257171.1 DL86_RS00215 3-deoxy-7-phosphoheptulonate synthase class II
Query= BRENDA::P29976 (525 letters) >NCBI__GCF_000746085.1:WP_036257171.1 Length = 462 Score = 536 bits (1380), Expect = e-157 Identities = 261/450 (58%), Positives = 328/450 (72%), Gaps = 1/450 (0%) Query: 75 WTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKAFLL 134 W+P SW+ K Q+PDY +A L V + FPP+VFAGEAR L+ L A G+AFLL Sbjct: 6 WSPASWRGKPIEQVPDYADAAALAEVEGQLAGFPPLVFAGEARKLKRMLGKVAAGEAFLL 65 Query: 135 QGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAFEEK 194 QGGDCAESF E +A NIRD FRV LQMS+V TF +PV+KVGR+AGQFAKPRS E+ Sbjct: 66 QGGDCAESFAEHSADNIRDFFRVFLQMSVVATFAAALPVVKVGRIAGQFAKPRSAPNEKL 125 Query: 195 DGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQRVTQ 254 V+LPSY+GD IN F + RIPDP R + AY QSAATLNLLRAFATGGYA ++ + Sbjct: 126 GDVELPSYRGDIINDIAFAAQGRIPDPARQLMAYRQSAATLNLLRAFATGGYANLENAHR 185 Query: 255 WNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTD-HPLMTTTDFYTSHECLLLPYEQ 313 W L F++ S Q+ RYQELA+R+ E LGFM A GL + H + TDFYTSHE LLL +E+ Sbjct: 186 WMLGFIKDSPQSARYQELADRITETLGFMRAIGLDPESHQELRQTDFYTSHEALLLGFEE 245 Query: 314 SLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFELVKL 373 +LTR+DST+G YY S HM+W G+RTRQ AH+E+ RG+ NPLG+K + P EL+ L Sbjct: 246 ALTRIDSTTGDYYATSGHMIWIGDRTRQPGHAHIEYARGVKNPLGLKCGPSLGPDELLSL 305 Query: 374 VEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAPCGL 433 ++ILNP N+PGR+T+I R GA+ LP LIRAV+R G+ V W CDPMHGNT+KA G Sbjct: 306 IDILNPANEPGRLTLICRFGADKAGDHLPGLIRAVKREGRSVVWSCDPMHGNTVKAASGF 365 Query: 434 KTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRYHTH 493 KTR FD I++E+R F H+ EG++AGG+HLEMTG+NVTECIGG+R ++ DL RYHT+ Sbjct: 366 KTRPFDKIMSEIRTFFSAHQAEGTYAGGVHLEMTGKNVTECIGGARAISEADLHDRYHTY 425 Query: 494 CDPRLNASQSLELAFIVAERLRKRRTGSQR 523 CDPRLNA Q++E+AF+VAE L+ R G R Sbjct: 426 CDPRLNAEQAIEVAFLVAELLKTERIGRGR 455 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: 660 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: 525 Length of database: 462 Length adjustment: 34 Effective length of query: 491 Effective length of database: 428 Effective search space: 210148 Effective search space used: 210148 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 WP_036257171.1 DL86_RS00215 (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.27939.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-213 693.2 0.0 6.5e-213 693.0 0.0 1.0 1 lcl|NCBI__GCF_000746085.1:WP_036257171.1 DL86_RS00215 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000746085.1:WP_036257171.1 DL86_RS00215 3-deoxy-7-phosphoheptulonate synthase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 693.0 0.0 6.5e-213 6.5e-213 1 442 [. 6 449 .. 6 450 .. 0.99 Alignments for each domain: == domain 1 score: 693.0 bits; conditional E-value: 6.5e-213 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 ws++swr kp q+P+y da+al +v+ +l+ +PPlv+age++klk+ l++va+GeafllqgGdcaesf lcl|NCBI__GCF_000746085.1:WP_036257171.1 6 WSPASWRGKPIEQVPDYADAAALAEVEGQLAGFPPLVFAGEARKLKRMLGKVAAGEAFLLQGGDCAESF 74 89******************************************************************* PP TIGR01358 70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138 e +adnird +rv+lqm+vv t++a lPvvkvgriaGq+akPrs+p e+ ++v+lpsyrGd+in af lcl|NCBI__GCF_000746085.1:WP_036257171.1 75 AEHSADNIRDFFRVFLQMSVVATFAAALPVVKVGRIAGQFAKPRSAPNEKLGDVELPSYRGDIINDIAF 143 ********************************************************************* PP TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207 ++ r+pdp r + ay +saatlnllra+++gGya+l++ h+W l f+k+sp++ary++la++i+e+l lcl|NCBI__GCF_000746085.1:WP_036257171.1 144 AAQGRIPDPARQLMAYRQSAATLNLLRAFATGGYANLENAHRWMLGFIKDSPQSARYQELADRITETLG 212 ********************************************************************* PP TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274 fm+a+g+++++ +l+++++ytshealll +eealtr ds++g+++ +s+h++WiG+rtrq +ah+e+ lcl|NCBI__GCF_000746085.1:WP_036257171.1 213 FMRAIGLDPEShqELRQTDFYTSHEALLLGFEEALTRIDSTTGDYYATSGHMIWIGDRTRQPGHAHIEY 281 ********987789******************************************************* PP TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343 +rgvknP+g+k+gps+ +dell li++l+P nePGrltli r+Ga+k ++lP l++avk++Gr+vvW lcl|NCBI__GCF_000746085.1:WP_036257171.1 282 ARGVKNPLGLKCGPSLGPDELLSLIDILNPANEPGRLTLICRFGADKAGDHLPGLIRAVKREGRSVVWS 350 ********************************************************************* PP TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412 +dpmhGnt++aasG+ktr fd+i+se+++ff h+aeGt+ GGvhle+tG++vtec+GGar+i+e dl+ lcl|NCBI__GCF_000746085.1:WP_036257171.1 351 CDPMHGNTVKAASGFKTRPFDKIMSEIRTFFSAHQAEGTYAGGVHLEMTGKNVTECIGGARAISEADLH 419 ********************************************************************* PP TIGR01358 413 sryetacdPrlnaeqslelaflvaeklrea 442 +ry+t cdPrlnaeq++e+aflvae l+ + lcl|NCBI__GCF_000746085.1:WP_036257171.1 420 DRYHTYCDPRLNAEQAIEVAFLVAELLKTE 449 **************************9975 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.15 // [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