Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate Ga0059261_0258 Ga0059261_0258 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54)
Query= BRENDA::P29976 (525 letters) >FitnessBrowser__Korea:Ga0059261_0258 Length = 527 Score = 543 bits (1399), Expect = e-159 Identities = 265/446 (59%), Positives = 333/446 (74%), Gaps = 1/446 (0%) Query: 72 ALKWTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKA 131 A+ WTP+SWK +A QLP YP+ L + + +FPP+VFAGEAR L + LA A G+A Sbjct: 73 AMGWTPDSWKSAEARQLPIYPDTATLAAATTQLSSFPPLVFAGEARALTQELAKVARGEA 132 Query: 132 FLLQGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAF 191 FLLQGGDCAESF EF+ NIRDTFRV+LQM++VLTF ++P +KVGRMAGQFAKPRS Sbjct: 133 FLLQGGDCAESFAEFHPNNIRDTFRVILQMAVVLTFASKLPTVKVGRMAGQFAKPRSADT 192 Query: 192 EEKDGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQR 251 E +GV+LPSY+GDN+N F ++RIPDP RMI+ Y+QSAATLNLLRAFA+GGYA + + Sbjct: 193 ETINGVELPSYRGDNVNDIAFTPEARIPDPQRMIQGYSQSAATLNLLRAFASGGYANLHQ 252 Query: 252 VTQWNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTDH-PLMTTTDFYTSHECLLLP 310 V +W LDF+ +S + ++ ++A+R+ EAL FM ACG+ D P + TDFYTSHE LLLP Sbjct: 253 VHKWTLDFMGKSPWSAKFADVADRIGEALDFMQACGIDADSVPQLKGTDFYTSHEALLLP 312 Query: 311 YEQSLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFEL 370 YEQ+LTR DS +G +YD SAHM+W G+RTR AHVEFLRGI NP+G+K ++P L Sbjct: 313 YEQALTRQDSLTGDWYDTSAHMLWIGDRTRFDGSAHVEFLRGIGNPIGMKCGPSLEPDAL 372 Query: 371 VKLVEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAP 430 ++L++ LNP PGR+T+I R G + + LP L+RAV+R G V W CDPMHGN +KA Sbjct: 373 LRLLDTLNPARTPGRLTLITRYGHDKIEDGLPKLVRAVKREGHPVVWSCDPMHGNVVKAA 432 Query: 431 CGLKTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRY 490 G KTR F+ ILAEVR F VH EG++AGGIH EMTGQNVTEC GG V+ DL+ RY Sbjct: 433 NGYKTRPFERILAEVRGFFAVHRAEGTYAGGIHAEMTGQNVTECTGGMIDVSEHDLADRY 492 Query: 491 HTHCDPRLNASQSLELAFIVAERLRK 516 HTHCDPRLNA QSLELAF++AE L + Sbjct: 493 HTHCDPRLNAGQSLELAFLLAEMLNE 518 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: 723 Number of extensions: 19 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: 527 Length adjustment: 35 Effective length of query: 490 Effective length of database: 492 Effective search space: 241080 Effective search space used: 241080 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 Ga0059261_0258 Ga0059261_0258 (3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54))
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.16819.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-215 699.1 0.0 1.2e-214 698.8 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0258 Ga0059261_0258 3-deoxy-D-arabino Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0258 Ga0059261_0258 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5. # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 698.8 0.0 1.2e-214 1.2e-214 1 441 [. 76 518 .. 76 520 .. 0.99 Alignments for each domain: == domain 1 score: 698.8 bits; conditional E-value: 1.2e-214 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 w+++sw+s +a qlP yPd+++l a +++l+s+PPlv+age+++l ++la+va+GeafllqgGdcaesf lcl|FitnessBrowser__Korea:Ga0059261_0258 76 WTPDSWKSAEARQLPIYPDTATLAAATTQLSSFPPLVFAGEARALTQELAKVARGEAFLLQGGDCAESF 144 89******************************************************************* PP TIGR01358 70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138 e++ +nird++rv+lqmavvlt++++lP vkvgr+aGq+akPrs+++e+ +gv+lpsyrGd++n af lcl|FitnessBrowser__Korea:Ga0059261_0258 145 AEFHPNNIRDTFRVILQMAVVLTFASKLPTVKVGRMAGQFAKPRSADTETINGVELPSYRGDNVNDIAF 213 ********************************************************************* PP TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207 + +ar+pdp+r+++ y++saatlnllra++sgGya+l++vh+W+l+f++ksp +a++ ++a++i+eal lcl|FitnessBrowser__Korea:Ga0059261_0258 214 TPEARIPDPQRMIQGYSQSAATLNLLRAFASGGYANLHQVHKWTLDFMGKSPWSAKFADVADRIGEALD 282 ********************************************************************* PP TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274 fm+a+g++ ++ +lk +++ytshealll+ye+altr+ds +g+++d+sah+lWiG+rtr ahvef lcl|FitnessBrowser__Korea:Ga0059261_0258 283 FMQACGIDADSvpQLKGTDFYTSHEALLLPYEQALTRQDSLTGDWYDTSAHMLWIGDRTRFDGSAHVEF 351 *******9999899**********************************************9889***** PP TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343 lrg+ nPig+k+gps+e+d ll+l++ l+P + PGrltli+r G +ki + lP+l++avk++G+ vvW lcl|FitnessBrowser__Korea:Ga0059261_0258 352 LRGIGNPIGMKCGPSLEPDALLRLLDTLNPARTPGRLTLITRYGHDKIEDGLPKLVRAVKREGHPVVWS 420 ********************************************************************* PP TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412 +dpmhGn ++aa+Gyktr f++il+ev++ff+vh+aeGt+ GG+h e+tG++vtec+GG +++e+dla lcl|FitnessBrowser__Korea:Ga0059261_0258 421 CDPMHGNVVKAANGYKTRPFERILAEVRGFFAVHRAEGTYAGGIHAEMTGQNVTECTGGMIDVSEHDLA 489 ********************************************************************* PP TIGR01358 413 sryetacdPrlnaeqslelaflvaeklre 441 +ry+t+cdPrlna qslelafl+ae+l+e lcl|FitnessBrowser__Korea:Ga0059261_0258 490 DRYHTHCDPRLNAGQSLELAFLLAEMLNE 518 **************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (527 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: 10.69 // [ok]
This GapMind analysis is from Apr 09 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