Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_046010086.1 OLEAN_RS16240 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P00888 (356 letters) >NCBI__GCF_000967895.1:WP_046010086.1 Length = 366 Score = 337 bits (865), Expect = 2e-97 Identities = 177/338 (52%), Positives = 226/338 (66%), Gaps = 6/338 (1%) Query: 17 LMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHDPETALEYARR 76 L TP QLK A PLS + Q+ R+ I ++ G D RLL++ GPCS+HDP LEY +R Sbjct: 29 LPTPRQLKQALPLSEALQRQVDQQRQQIRQLLQGEDDRLLIITGPCSLHDPVAVLEYGQR 88 Query: 77 FKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQIARKLLLELVN 136 AL ++SD L +VMR Y EKPRTT GWKGL DP +G+ D++ GL+++R LLL+LV Sbjct: 89 LVALNEQLSDRLLIVMRAYVEKPRTTTGWKGLAYDPDRNGAGDIKKGLEVSRSLLLQLVE 148 Query: 137 MGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGFKNGTDGSLAT 196 MGLPLATEAL+P + YL DL SW+AIGART ESQ HREM S LSMPVG KNGTDGS+ T Sbjct: 149 MGLPLATEALNPMTMSYLEDLISWTAIGARTAESQIHREMISHLSMPVGIKNGTDGSVDT 208 Query: 197 AINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGK-APNYSPAD----VAQCE 251 A+NAM +A++ H +G + G +A+L T GN D HV+LRGG+ NY VAQ + Sbjct: 209 AVNAMISASRSHHCLGTDVDGNIAMLDTPGNSDTHVVLRGGRNLTNYDDISIQNAVAQLD 268 Query: 252 KEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESNIHEGNQ 311 K L ++VDCSH N+ K + RQ +A VV Q GN +I GLMIES I+ GNQ Sbjct: 269 KAKTDNQLHAKVIVDCSHDNAQKQHDRQLDIALQVVQQRIAGNNAISGLMIESFINMGNQ 328 Query: 312 SSEQPRSE-MKYGVSVTDACISWEMTDALLREIHQDLN 348 + P ++ + YGVS+TD CISW T+ LL IHQ L+ Sbjct: 329 GMKGPNNQGLDYGVSITDPCISWNQTEMLLTNIHQLLS 366 Lambda K H 0.316 0.131 0.378 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: 380 Number of extensions: 9 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: 356 Length of database: 366 Length adjustment: 29 Effective length of query: 327 Effective length of database: 337 Effective search space: 110199 Effective search space used: 110199 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_046010086.1 OLEAN_RS16240 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR00034 (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/TIGR00034.hmm # target sequence database: /tmp/gapView.10544.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00034 [M=342] Accession: TIGR00034 Description: aroFGH: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-134 433.1 0.3 3.4e-134 432.9 0.3 1.0 1 lcl|NCBI__GCF_000967895.1:WP_046010086.1 OLEAN_RS16240 3-deoxy-7-phosphoh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000967895.1:WP_046010086.1 OLEAN_RS16240 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 432.9 0.3 3.4e-134 3.4e-134 5 336 .. 23 363 .. 19 366 .] 0.96 Alignments for each domain: == domain 1 score: 432.9 bits; conditional E-value: 3.4e-134 TIGR00034 5 ivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkk 73 +++ +l tP++lk++ pl+e+ + +v ++r++i ++l+G+ddrll++ GPcs+hdp a ley +rl + lcl|NCBI__GCF_000967895.1:WP_046010086.1 23 LAAVRPLPTPRQLKQALPLSEALQRQVDQQRQQIRQLLQGEDDRLLIITGPCSLHDPVAVLEYGQRLVA 91 567899*************************************************************** PP TIGR00034 74 laeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldt 142 l+e+l+d+l ivmr+y+ekPrtt GWkGl dPd n++ d++kGl+++r lll+lve+glplate+l++ lcl|NCBI__GCF_000967895.1:WP_046010086.1 92 LNEQLSDRLLIVMRAYVEKPRTTTGWKGLAYDPDRNGAGDIKKGLEVSRSLLLQLVEMGLPLATEALNP 160 ********************************************************************* PP TIGR00034 143 ispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaG 211 ++ yl dl+sw+aiGart+esq+hre+ s ls+pvg kngtdGs+ +a++a+ +a+++h+ l+++ +G lcl|NCBI__GCF_000967895.1:WP_046010086.1 161 MTMSYLEDLISWTAIGARTAESQIHREMISHLSMPVGIKNGTDGSVDTAVNAMISASRSHHCLGTDVDG 229 ********************************************************************* PP TIGR00034 212 qvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkee....lmidfshgnsnkdykrqle 275 ++a+++t Gn+d+h++lrGG++ +nyd +++++ ++l+ka++ ++ +++d+sh n++k++ rql+ lcl|NCBI__GCF_000967895.1:WP_046010086.1 230 NIAMLDTPGNSDTHVVLRGGRNlTNYDDISIQNAVAQLDKAKTDNQlhakVIVDCSHDNAQKQHDRQLD 298 ***************************************987665544459****************** PP TIGR00034 276 vaesvveqiaeGekaiiGvmiesnleeGnqsl....keelkyGksvtdacigwedteallrklae 336 +a +vv+q G++ai G+mies+++ Gnq + +++l yG+s+td ci+w++te ll ++++ lcl|NCBI__GCF_000967895.1:WP_046010086.1 299 IALQVVQQRIAGNNAISGLMIESFINMGNQGMkgpnNQGLDYGVSITDPCISWNQTEMLLTNIHQ 363 ******************************985555689***********************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (366 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: 7.07 // [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