Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_084275589.1 B8779_RS05750 3-deoxy-7-phosphoheptulonate synthase class II
Query= BRENDA::P29976 (525 letters) >NCBI__GCF_900176045.1:WP_084275589.1 Length = 447 Score = 507 bits (1305), Expect = e-148 Identities = 244/445 (54%), Positives = 330/445 (74%), Gaps = 2/445 (0%) Query: 73 LKWTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKAF 132 + W+P SW+ Q P Y + ++L S+ I+ FPP++FAGEAR L++ LA A G+A Sbjct: 1 MSWSPSSWRDFPIKQQPTYKDLDKLHSIEAEIKTFPPLIFAGEARELKKDLAKVAKGEAI 60 Query: 133 LLQGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAFE 192 LLQGGDCAESF FNA NIRD F+VLLQM++VL + PV+K+GR+AGQ+AKPRS +E Sbjct: 61 LLQGGDCAESFANFNAANIRDLFKVLLQMNMVLMYATGKPVVKIGRIAGQYAKPRSSDYE 120 Query: 193 EKDGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQRV 252 E GVKLPSY+GD +N F E++R P P +++ AY +SAATLNL+RA+A GG+A ++ V Sbjct: 121 EIGGVKLPSYRGDIVNDIAFSEEAREPKPEKLLEAYYKSAATLNLIRAYARGGFADLRAV 180 Query: 253 TQWNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTDH-PLMTTTDFYTSHECLLLPY 311 +WNL+F++ +E R++ELA+++ EAL FM ACG+ D+ P + T YTSHE LLL Y Sbjct: 181 HKWNLEFLQGNELESRFEELADKITEALRFMEACGVNPDNTPQLKQTTLYTSHEALLLNY 240 Query: 312 EQSLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFELV 371 E++LTR D+ +G +YDCSAH +W G+RTR +GAHVEF RGI NP+G+KV M P EL+ Sbjct: 241 EEALTRKDTFTGDWYDCSAHFLWIGDRTRDPNGAHVEFFRGIKNPIGVKVGPSMKPHELL 300 Query: 372 KLVEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAPC 431 +L++ LNP N+PGR+T+IVRMGAE + P L+R V+ +G+ V W DPMHGNT K Sbjct: 301 ELIDKLNPENEPGRLTLIVRMGAEKIGELFPPLLRTVKEAGKEVVWSIDPMHGNTYKTGG 360 Query: 432 GLKTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGG-SRTVTYDDLSSRY 490 GLKTR F+ IL+EV+ F+ +H+ EG+ GG+HLEMTG +VTEC G S ++T D L+SRY Sbjct: 361 GLKTRDFEKILSEVKQFIQIHKAEGTVPGGMHLEMTGSDVTECTGSISASITEDALNSRY 420 Query: 491 HTHCDPRLNASQSLELAFIVAERLR 515 HT CDPRLNA+Q+LELAF+VAE + Sbjct: 421 HTQCDPRLNANQALELAFMVAETFK 445 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: 631 Number of extensions: 28 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: 525 Length of database: 447 Length adjustment: 34 Effective length of query: 491 Effective length of database: 413 Effective search space: 202783 Effective search space used: 202783 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_084275589.1 B8779_RS05750 (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.15140.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-209 680.8 0.0 3.8e-209 680.6 0.0 1.0 1 lcl|NCBI__GCF_900176045.1:WP_084275589.1 B8779_RS05750 3-deoxy-7-phosphoh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176045.1:WP_084275589.1 B8779_RS05750 3-deoxy-7-phosphoheptulonate synthase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 680.6 0.0 3.8e-209 3.8e-209 1 441 [. 3 446 .. 3 447 .] 0.99 Alignments for each domain: == domain 1 score: 680.6 bits; conditional E-value: 3.8e-209 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 ws++swr+ p +q+P+y d ++l++++++++++PPl++age+++lk+ la+vakGea llqgGdcaesf lcl|NCBI__GCF_900176045.1:WP_084275589.1 3 WSPSSWRDFPIKQQPTYKDLDKLHSIEAEIKTFPPLIFAGEARELKKDLAKVAKGEAILLQGGDCAESF 71 89******************************************************************* PP TIGR01358 70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138 +++a+nird ++vllqm +vl+y++++Pvvk+griaGqyakPrs++ e+ +gv+lpsyrGd++n af lcl|NCBI__GCF_900176045.1:WP_084275589.1 72 ANFNAANIRDLFKVLLQMNMVLMYATGKPVVKIGRIAGQYAKPRSSDYEEIGGVKLPSYRGDIVNDIAF 140 ********************************************************************* PP TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207 +e+ar+p pe+l++ay ksaatlnl+ra++ gG+adl+ vh+Wnlef + + +r+e+la++i+ealr lcl|NCBI__GCF_900176045.1:WP_084275589.1 141 SEEAREPKPEKLLEAYYKSAATLNLIRAYARGGFADLRAVHKWNLEFLQGNELESRFEELADKITEALR 209 ********************************************************************* PP TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274 fm+a+gv++++ +lk++ lytshealll+yeealtr+d +g+++d+sah+lWiG+rtr +gahvef lcl|NCBI__GCF_900176045.1:WP_084275589.1 210 FMEACGVNPDNtpQLKQTTLYTSHEALLLNYEEALTRKDTFTGDWYDCSAHFLWIGDRTRDPNGAHVEF 278 ********999899******************************************************* PP TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343 rg+knPig+kvgpsm+++ell+li++l+PenePGrltli+r+Gaeki e++P+ll+ vk+aG++vvW lcl|NCBI__GCF_900176045.1:WP_084275589.1 279 FRGIKNPIGVKVGPSMKPHELLELIDKLNPENEPGRLTLIVRMGAEKIGELFPPLLRTVKEAGKEVVWS 347 ********************************************************************* PP TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGG.areitetdl 411 dpmhGnt+++++G+ktr f++ilsevk+f+++hkaeGt pGG+hle+tG dvtec+G + +ite+ l lcl|NCBI__GCF_900176045.1:WP_084275589.1 348 IDPMHGNTYKTGGGLKTRDFEKILSEVKQFIQIHKAEGTVPGGMHLEMTGSDVTECTGSiSASITEDAL 416 **********************************************************98899****** PP TIGR01358 412 asryetacdPrlnaeqslelaflvaeklre 441 +sry+t+cdPrlna+q+lelaf+vae++++ lcl|NCBI__GCF_900176045.1:WP_084275589.1 417 NSRYHTQCDPRLNANQALELAFMVAETFKD 446 **************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (447 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.97 // [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