Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011938638.1 GURA_RS08820 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P00888 (356 letters) >NCBI__GCF_000016745.1:WP_011938638.1 Length = 354 Score = 407 bits (1047), Expect = e-118 Identities = 196/341 (57%), Positives = 254/341 (74%) Query: 7 NNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHD 66 NN+ I ++ P L+ FP+S + ++ SR++I +I+ G+DPRL+VV GPCSIHD Sbjct: 5 NNLKIKSITPIIAPTDLRQVFPISAEASECVSASRENIKNILKGKDPRLMVVVGPCSIHD 64 Query: 67 PETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQI 126 P+ ALEYA R L+ EVSD L LVMRVYFEKPRTTVGWKGLINDP M+G+ + GL I Sbjct: 65 PKGALEYAERLARLSKEVSDQLLLVMRVYFEKPRTTVGWKGLINDPDMNGTHLISKGLGI 124 Query: 127 ARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGF 186 AR+LL E+ M LP+ATE LDP +P+YL D SW AIGARTTESQTHRE+ASGLS P+GF Sbjct: 125 ARRLLSEITAMKLPIATEMLDPITPEYLADHLSWGAIGARTTESQTHRELASGLSFPIGF 184 Query: 187 KNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKAPNYSPAD 246 KNGTDG+L AI+AM AA H F+GIN+ G +++QT GNPD H++LRGGK PNY P D Sbjct: 185 KNGTDGNLQIAIDAMIAAQHSHSFLGINREGLTSIVQTTGNPDVHMVLRGGKKPNYYPED 244 Query: 247 VAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESNI 306 +A E+++ +AGL P++MVDCSHGNS K++ +QP V E+V+ QI GNRSI +MIES + Sbjct: 245 IALTEEKLGKAGLSPTIMVDCSHGNSEKNHEKQPLVLENVIEQIAAGNRSISSVMIESYL 304 Query: 307 HEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDL 347 GNQ + S++KYGVS+TD CI W+ T+A++R+ H L Sbjct: 305 EGGNQPMPKDISQLKYGVSITDKCIDWQTTEAIMRKAHASL 345 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: 411 Number of extensions: 13 Number of successful extensions: 1 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: 354 Length adjustment: 29 Effective length of query: 327 Effective length of database: 325 Effective search space: 106275 Effective search space used: 106275 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_011938638.1 GURA_RS08820 (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.1175056.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-159 513.7 0.0 1.1e-158 513.4 0.0 1.0 1 NCBI__GCF_000016745.1:WP_011938638.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000016745.1:WP_011938638.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 513.4 0.0 1.1e-158 1.1e-158 2 339 .. 6 346 .. 5 348 .. 0.98 Alignments for each domain: == domain 1 score: 513.4 bits; conditional E-value: 1.1e-158 TIGR00034 2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkkl 74 +l+i++i ++++P++l++ fp++++a e v sr++i++il+Gkd+rl+vv+GPcsihdp+ aleya+rl++l NCBI__GCF_000016745.1:WP_011938638.1 6 NLKIKSITPIIAPTDLRQVFPISAEASECVSASRENIKNILKGKDPRLMVVVGPCSIHDPKGALEYAERLARL 78 7899********************************************************************* PP TIGR00034 75 aeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqy 147 +++++d+l +vmrvyfekPrttvGWkGlindPd+n+++ + kGl iar+ll +++ + lp+ate+ld+i+p y NCBI__GCF_000016745.1:WP_011938638.1 79 SKEVSDQLLLVMRVYFEKPRTTVGWKGLINDPDMNGTHLISKGLGIARRLLSEITAMKLPIATEMLDPITPEY 151 ************************************************************************* PP TIGR00034 148 ladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkG 220 lad lswgaiGarttesq+hrelasgls+p+gfkngtdG+l++aida+ aa+++h fl+++++G ++iv+t+G NCBI__GCF_000016745.1:WP_011938638.1 152 LADHLSWGAIGARTTESQTHRELASGLSFPIGFKNGTDGNLQIAIDAMIAAQHSHSFLGINREGLTSIVQTTG 224 ************************************************************************* PP TIGR00034 221 nedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiG 293 n+d h++lrGGkkpny +ed+a ++e+l kagl++++m+d+shgns+k++++q+ v e+v+eqia G+++i NCBI__GCF_000016745.1:WP_011938638.1 225 NPDVHMVLRGGKKPNYYPEDIALTEEKLGKAGLSPTIMVDCSHGNSEKNHEKQPLVLENVIEQIAAGNRSISS 297 ************************************************************************* PP TIGR00034 294 vmiesnleeGnqsl...keelkyGksvtdacigwedteallrklaeavk 339 vmies+le+Gnq + ++lkyG+s+td+ci+w++tea++rk ++++k NCBI__GCF_000016745.1:WP_011938638.1 298 VMIESYLEGGNQPMpkdISQLKYGVSITDKCIDWQTTEAIMRKAHASLK 346 ************996434689**********************998776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (354 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 24.93 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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