Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_004513245.1 GMET_RS11970 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P00888 (356 letters) >NCBI__GCF_000012925.1:WP_004513245.1 Length = 355 Score = 400 bits (1027), Expect = e-116 Identities = 190/341 (55%), Positives = 254/341 (74%) Query: 7 NNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHD 66 +N+ +T ++ P L+ FP SL+ + SR I +I+ G+D RL+VV GPCSIHD Sbjct: 5 SNLKVTSITPIIAPADLRQVFPQSLETAEFVNASRAHIKNILKGKDTRLMVVVGPCSIHD 64 Query: 67 PETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQI 126 P+ AL+YA R LA+E+SD L++VMRVYFEKPRTT+GWKGLINDP M+ + + GL I Sbjct: 65 PKAALDYAGRLARLASELSDQLFIVMRVYFEKPRTTIGWKGLINDPDMNHTHQISKGLGI 124 Query: 127 ARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGF 186 AR+LL ++ +M LP+A E LD +P+YL D SW AIGARTTESQ+HREMASGLS PVGF Sbjct: 125 ARRLLNDITSMLLPVACEMLDTITPEYLADYISWGAIGARTTESQSHREMASGLSFPVGF 184 Query: 187 KNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKAPNYSPAD 246 KNGTDG+L AI+AM AA PH F+GIN+ G+ +++QT GNPD H++LRGGK PNYSP D Sbjct: 185 KNGTDGNLQIAIDAMNAALHPHSFLGINRDGKTSIIQTTGNPDVHIVLRGGKKPNYSPED 244 Query: 247 VAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESNI 306 +A+ E+ +E+ G+ P++MVDCSHGNS K + +QP V +S+V QI+ GNRSI G+MIES + Sbjct: 245 IAKTEEMVEKGGIFPTIMVDCSHGNSEKRHEKQPEVLDSIVDQIEAGNRSISGVMIESFL 304 Query: 307 HEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDL 347 GNQ + S+++YGVS TD CI W+ T+ +LR+ H+ L Sbjct: 305 EAGNQPIPKDLSQLRYGVSTTDKCIDWKTTEEILRKAHERL 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: 412 Number of extensions: 14 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: 355 Length adjustment: 29 Effective length of query: 327 Effective length of database: 326 Effective search space: 106602 Effective search space used: 106602 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_004513245.1 GMET_RS11970 (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.16787.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-159 515.7 0.0 2.7e-159 515.4 0.0 1.0 1 lcl|NCBI__GCF_000012925.1:WP_004513245.1 GMET_RS11970 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012925.1:WP_004513245.1 GMET_RS11970 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 515.4 0.0 2.7e-159 2.7e-159 2 339 .. 6 346 .. 5 348 .. 0.98 Alignments for each domain: == domain 1 score: 515.4 bits; conditional E-value: 2.7e-159 TIGR00034 2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakr 70 +l++++i ++++P++l++ fp + ++ae v+ sr +i++il+Gkd+rl+vv+GPcsihdp+aal+ya r lcl|NCBI__GCF_000012925.1:WP_004513245.1 6 NLKVTSITPIIAPADLRQVFPQSLETAEFVNASRAHIKNILKGKDTRLMVVVGPCSIHDPKAALDYAGR 74 688999*************************************************************** PP TIGR00034 71 lkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatel 139 l++la++l+d+l ivmrvyfekPrtt+GWkGlindPd+n+++++ kGl iar+ll d++ + lp+a+e+ lcl|NCBI__GCF_000012925.1:WP_004513245.1 75 LARLASELSDQLFIVMRVYFEKPRTTIGWKGLINDPDMNHTHQISKGLGIARRLLNDITSMLLPVACEM 143 ********************************************************************* PP TIGR00034 140 ldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvt 208 ldti+p ylad +swgaiGarttesq hre+asgls+pvgfkngtdG+l++aida++aa ++h fl+++ lcl|NCBI__GCF_000012925.1:WP_004513245.1 144 LDTITPEYLADYISWGAIGARTTESQSHREMASGLSFPVGFKNGTDGNLQIAIDAMNAALHPHSFLGIN 212 ********************************************************************* PP TIGR00034 209 kaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqleva 277 ++G+++i++t+Gn+d hi+lrGGkkpny++ed+a+++e +ek g +++m+d+shgns+k +++q+ev lcl|NCBI__GCF_000012925.1:WP_004513245.1 213 RDGKTSIIQTTGNPDVHIVLRGGKKPNYSPEDIAKTEEMVEKGGIFPTIMVDCSHGNSEKRHEKQPEVL 281 ********************************************************************* PP TIGR00034 278 esvveqiaeGekaiiGvmiesnleeGnqsl...keelkyGksvtdacigwedteallrklaeavk 339 +s+v+qi+ G+++i Gvmies+le Gnq + ++l yG+s td+ci+w++te++lrk +e +k lcl|NCBI__GCF_000012925.1:WP_004513245.1 282 DSIVDQIEAGNRSISGVMIESFLEAGNQPIpkdLSQLRYGVSTTDKCIDWKTTEEILRKAHERLK 346 *****************************953335789*********************998775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (355 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: 7.89 // [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