Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_012383758.1 BIND_RS03835 3-deoxy-7-phosphoheptulonate synthase class II
Query= BRENDA::A0A0D5ZBC4 (539 letters) >NCBI__GCF_000019845.1:WP_012383758.1 Length = 462 Score = 526 bits (1355), Expect = e-154 Identities = 260/450 (57%), Positives = 328/450 (72%), Gaps = 1/450 (0%) Query: 83 WTVDSWKSKKALQLPEYPDQAELESVLKTLDAFPPIVFAGEARSLEEKLGEAAMGNAFLL 142 W+ SW++K +Q+PE+ D A+L V L FPP+VFAGEAR L+ LG+ A G AFLL Sbjct: 6 WSPASWRNKPIVQVPEFTDAAKLADVEGQLAGFPPLVFAGEARKLKSLLGKVADGEAFLL 65 Query: 143 QGGDCAESFKEFNANNIRDTFRILLQMGAVLMFGGQMPVIKVGRMAGQFAKPRSDPFEEK 202 QGGDCAESF E +A+NIRD FR+ LQM V F +PV+KVGR+AGQFAKPRS P E+ Sbjct: 66 QGGDCAESFAEHHADNIRDFFRVFLQMAVVATFAAALPVVKVGRIAGQFAKPRSAPNEKV 125 Query: 203 NGVKLPSYRGDNVNGDSFDEKSRIPDPQRMIRAYCQSAATLNLLRAFATGGYAAMQRVTQ 262 V+LPSYRGD VN +FD +R PDP R + AY QSAATLNLLRAFATGGYA ++ + Sbjct: 126 GDVELPSYRGDIVNDIAFDSAAREPDPVRQLMAYRQSAATLNLLRAFATGGYANLENAHR 185 Query: 263 WNLDFTEHSEQGDRYRELASRVDEALGFMAAAGLTVD-HPIMTTTEFWTSHECLLLPYEQ 321 W L F S Q RY+ELA R+ E LGFM A GL + H + T+F+TSHE LLL YE+ Sbjct: 186 WMLGFVSDSPQSARYQELADRITETLGFMRAIGLDPESHHELRQTDFFTSHEALLLGYEE 245 Query: 322 SLTRLDSTSGRYYDCSAHFLWAGERTRQLDGAHVEFLRGVANPLGIKVSDKMDPNELVKL 381 +LTR+DSTSG YY S H LW G+RTR AHVE+ RGV NP+G+K + P++L++L Sbjct: 246 ALTRIDSTSGDYYATSGHMLWIGDRTRDPGQAHVEYARGVKNPIGLKCGPSLKPDDLLRL 305 Query: 382 IEILNPQNKAGRITVITRMGAENMRVKLPHLIRAVRRAGQIVTWVSDPMHGNTIKAPCGL 441 I++LNP N+AGR+T+I R GA+ + LP LIRAV++ G+ V W DPMHGNTIKA G Sbjct: 306 IDLLNPANEAGRLTLICRFGADKIGDHLPALIRAVQQEGRRVVWSCDPMHGNTIKAASGF 365 Query: 442 KTRPFDSIRAEVRAFFDVHEQEGSHPGGVHLEMTGQNVTECIGGSRTVTFDDLGSRYHTH 501 KTRPF+ I +E+R+FF VH EG++ GGVHLEMTG+NVTEC GG+R +T DL RYHT+ Sbjct: 366 KTRPFEKIMSEIRSFFAVHRAEGTYAGGVHLEMTGKNVTECTGGARAITDADLHDRYHTY 425 Query: 502 CDPRLNASQSLELAFIIAERLRKRRINSPQ 531 CDPRLNA QS+E+AF++AE L++ RI Q Sbjct: 426 CDPRLNAEQSIEVAFLVAELLKEERIGRGQ 455 Lambda K H 0.318 0.133 0.393 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: 672 Number of extensions: 23 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: 539 Length of database: 462 Length adjustment: 34 Effective length of query: 505 Effective length of database: 428 Effective search space: 216140 Effective search space used: 216140 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_012383758.1 BIND_RS03835 (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.4500.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-214 695.9 0.0 9.8e-214 695.7 0.0 1.0 1 lcl|NCBI__GCF_000019845.1:WP_012383758.1 BIND_RS03835 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019845.1:WP_012383758.1 BIND_RS03835 3-deoxy-7-phosphoheptulonate synthase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 695.7 0.0 9.8e-214 9.8e-214 1 442 [. 6 449 .. 6 450 .. 0.99 Alignments for each domain: == domain 1 score: 695.7 bits; conditional E-value: 9.8e-214 TIGR01358 1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 ws++swr+kp +q+Pe+ da++l v+ +l+ +PPlv+age++klk+ l++va GeafllqgGdcaesf lcl|NCBI__GCF_000019845.1:WP_012383758.1 6 WSPASWRNKPIVQVPEFTDAAKLADVEGQLAGFPPLVFAGEARKLKSLLGKVADGEAFLLQGGDCAESF 74 89******************************************************************* PP TIGR01358 70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138 e +adnird +rv+lqmavv t++a lPvvkvgriaGq+akPrs+p e+ ++v+lpsyrGd++n af lcl|NCBI__GCF_000019845.1:WP_012383758.1 75 AEHHADNIRDFFRVFLQMAVVATFAAALPVVKVGRIAGQFAKPRSAPNEKVGDVELPSYRGDIVNDIAF 143 ********************************************************************* PP TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207 d aar+pdp r + ay +saatlnllra+++gGya+l++ h+W l fv +sp++ary++la++i+e+l lcl|NCBI__GCF_000019845.1:WP_012383758.1 144 DSAAREPDPVRQLMAYRQSAATLNLLRAFATGGYANLENAHRWMLGFVSDSPQSARYQELADRITETLG 212 ********************************************************************* PP TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274 fm+a+g+++++ +l++++++tshealll yeealtr ds++g+++ +s+h+lWiG+rtr +ahve+ lcl|NCBI__GCF_000019845.1:WP_012383758.1 213 FMRAIGLDPEShhELRQTDFFTSHEALLLGYEEALTRIDSTSGDYYATSGHMLWIGDRTRDPGQAHVEY 281 *******9987779******************************************************* PP TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343 +rgvknPig+k+gps+++d+ll+li+ l+P ne Grltli r+Ga+ki ++lP l++av+++Gr+vvW lcl|NCBI__GCF_000019845.1:WP_012383758.1 282 ARGVKNPIGLKCGPSLKPDDLLRLIDLLNPANEAGRLTLICRFGADKIGDHLPALIRAVQQEGRRVVWS 350 ********************************************************************* PP TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412 +dpmhGnt++aasG+ktr f++i+se+++ff+vh+aeGt+ GGvhle+tG++vtec+GGar+it+ dl+ lcl|NCBI__GCF_000019845.1:WP_012383758.1 351 CDPMHGNTIKAASGFKTRPFEKIMSEIRSFFAVHRAEGTYAGGVHLEMTGKNVTECTGGARAITDADLH 419 ********************************************************************* PP TIGR01358 413 sryetacdPrlnaeqslelaflvaeklrea 442 +ry+t cdPrlnaeqs+e+aflvae l+e+ lcl|NCBI__GCF_000019845.1:WP_012383758.1 420 DRYHTYCDPRLNAEQSIEVAFLVAELLKEE 449 ***************************986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.07 # Mc/sec: 2.70 // [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