Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_015798229.1 AFER_RS04080 3-deoxy-7-phosphoheptulonate synthase class II
Query= BRENDA::O68903 (455 letters) >NCBI__GCF_000023265.1:WP_015798229.1 Length = 451 Score = 476 bits (1226), Expect = e-139 Identities = 241/448 (53%), Positives = 313/448 (69%), Gaps = 15/448 (3%) Query: 19 LDDALGRP-------AAQQPEWPDADLARRVRAVLESVPPITVPAEIDRLRENLAAVARG 71 LDDA +P AAQQPEWPD + V L P + V ++DRLR LA ARG Sbjct: 4 LDDAGWQPWDWQQRVAAQQPEWPDPEALDAVIKELAQRPALVVAKDVDRLRAALARAARG 63 Query: 72 EAFMLQGGDCAETFADNTEPHIRANVRTLLQMAVVLTYGASLPVVKIGRIAGQYAKPRSS 131 AF+LQ GDCAE+F D++ +RA ++ +LQMAVVLTY + + VVKIGRIAGQ+AKPRS+ Sbjct: 64 RAFVLQAGDCAESFHDHSASSLRAKLKIILQMAVVLTYSSGVSVVKIGRIAGQFAKPRSA 123 Query: 132 GT---DALGLPSYRGDIVNSLVPTPEARVADPGRMIRAYANAGAAMNLLRAMTTAGMADL 188 D LPS+RG IV+ PT +AR +P R++ AY + A +++LRA+T G ADL Sbjct: 124 PVEVVDGATLPSFRGHIVHDDAPTLDARRPNPERLLWAYDQSRATVSVLRALTEGGFADL 183 Query: 189 HRLHDWNKDFVRTSPAGERYEALAAEIDRGLRFMSACGVN---DSSLHTTEIFASHEALL 245 H WN DFV +SP G+RY+A+A +DR LRFM+ CG++ ++ LH ++ SHEALL Sbjct: 184 SGAHRWNLDFVASSPEGQRYQAIADGVDRALRFMAGCGIDLEREAVLHQVNVWTSHEALL 243 Query: 246 LDYERALLRLDTRGDEPKLYDLSSHFLWIGERTKQLDGAHIAFAELLANPIGLKIGPSTT 305 L YE AL R D + YDLS+H +W+GERT+QLDGAH+ FA +ANP+GLK+GP+ Sbjct: 244 LPYEAALTRRDPASQ--RYYDLSAHMVWVGERTRQLDGAHLRFASGIANPVGLKVGPTME 301 Query: 306 PEMAVEYVERLDPHNQPGRLTLIIRMGNGKVRDVLPAIVEKVTASGHKVIWQCDPMHGNT 365 P+ VE LDP PGRL LI RMG+ VRD L +VE V +G+ V+W CDPMHGNT Sbjct: 302 PDTLVEACRILDPDRTPGRLVLISRMGHDAVRDRLGGLVEAVREAGYPVVWLCDPMHGNT 361 Query: 366 HESSTGYKTRHFDRIVDEVQGFFEVHRRLGTHPGGIHIELTGEDVTECLGGAQEISDTDL 425 S +GYKTR F+ ++DE+ GFFEVHRRLGTH GGIH+ELTGEDVTECLGG++ + +++L Sbjct: 362 FVSQSGYKTRRFEDVMDEIAGFFEVHRRLGTHAGGIHLELTGEDVTECLGGSEAVLESEL 421 Query: 426 AGRYETACDPRLNTQQSLELAFLVAEML 453 Y+T CDPRLN +QSL+LAF VAE+L Sbjct: 422 CRAYDTICDPRLNARQSLDLAFRVAELL 449 Lambda K H 0.319 0.135 0.404 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: 566 Number of extensions: 23 Number of successful extensions: 4 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: 455 Length of database: 451 Length adjustment: 33 Effective length of query: 422 Effective length of database: 418 Effective search space: 176396 Effective search space used: 176396 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: 51 (24.3 bits)
Align candidate WP_015798229.1 AFER_RS04080 (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.23241.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-202 658.6 0.0 2e-202 658.5 0.0 1.0 1 lcl|NCBI__GCF_000023265.1:WP_015798229.1 AFER_RS04080 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023265.1:WP_015798229.1 AFER_RS04080 3-deoxy-7-phosphoheptulonate synthase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 658.5 0.0 2e-202 2e-202 1 439 [. 9 449 .. 9 451 .] 0.99 Alignments for each domain: == domain 1 score: 658.5 bits; conditional E-value: 2e-202 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 w++ w+++ aaq+Pe+Pd eal+av+++l++ P lv+a+++++l++ la++a+G+af+lq+Gdcaesf lcl|NCBI__GCF_000023265.1:WP_015798229.1 9 WQPWDWQQRVAAQQPEWPDPEALDAVIKELAQRPALVVAKDVDRLRAALARAARGRAFVLQAGDCAESF 77 67888**************************************************************** PP TIGR01358 70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138 ++ +a+++r kl+++lqmavvlty++++ vvk+griaGq+akPrs+p+e+ dg tlps+rG ++ +a+ lcl|NCBI__GCF_000023265.1:WP_015798229.1 78 HDHSASSLRAKLKIILQMAVVLTYSSGVSVVKIGRIAGQFAKPRSAPVEVVDGATLPSFRGHIVHDDAP 146 ********************************************************************* PP TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207 + +ar+p+perl+ ay +s at+ +lralt+gG+adl+ h+Wnl+fv +sp+g+ry+++a+ +d+alr lcl|NCBI__GCF_000023265.1:WP_015798229.1 147 TLDARRPNPERLLWAYDQSRATVSVLRALTEGGFADLSGAHRWNLDFVASSPEGQRYQAIADGVDRALR 215 ********************************************************************* PP TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274 fm +g++ ++ l++v+++tshealll+ye altr d+ +++++dlsah++W+Gertrqldgah+ f lcl|NCBI__GCF_000023265.1:WP_015798229.1 216 FMAGCGIDLEReaVLHQVNVWTSHEALLLPYEAALTRRDPASQRYYDLSAHMVWVGERTRQLDGAHLRF 284 ******99766579******************************************************* PP TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343 ++g++nP+g+kvgp+me+d l++ + +ldP++ PGrl+lisr+G + ++++l l+eav++aG vvW lcl|NCBI__GCF_000023265.1:WP_015798229.1 285 ASGIANPVGLKVGPTMEPDTLVEACRILDPDRTPGRLVLISRMGHDAVRDRLGGLVEAVREAGYPVVWL 353 ********************************************************************* PP TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412 +dpmhGnt+++ sGyktrrf+d+++e+++ffevh+ +Gth GG+hleltGedvteclGG+++++e++l lcl|NCBI__GCF_000023265.1:WP_015798229.1 354 CDPMHGNTFVSQSGYKTRRFEDVMDEIAGFFEVHRRLGTHAGGIHLELTGEDVTECLGGSEAVLESELC 422 ********************************************************************* PP TIGR01358 413 sryetacdPrlnaeqslelaflvaekl 439 ++y+t cdPrlna+qsl+laf vae l lcl|NCBI__GCF_000023265.1:WP_015798229.1 423 RAYDTICDPRLNARQSLDLAFRVAELL 449 ************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (451 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.91 // [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