Align Phospho-2-dehydro-3-deoxyheptonate aldolase, phenylalanine-inhibited; 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase; DAHP synthase; Phospho-2-keto-3-deoxyheptonate aldolase; EC 2.5.1.54 (characterized)
to candidate WP_092058003.1 BQ4888_RS14575 3-deoxy-7-phosphoheptulonate synthase
Query= SwissProt::P14843 (370 letters) >NCBI__GCF_900111775.1:WP_092058003.1 Length = 355 Score = 374 bits (961), Expect = e-108 Identities = 182/344 (52%), Positives = 244/344 (70%), Gaps = 7/344 (2%) Query: 12 KRLEDWRIKGYDPLTPPDLLQHEFPISAKGEENIIKARDSVCDILNGKDDRLVIVIGPCS 71 KR + RI+ P+ P L+ FP+S G E + +AR+ + +ILN KD RL++V+GPCS Sbjct: 2 KRTNNLRIRRTAPIIAPADLKQVFPLSEHGAEFVYQAREQITNILNHKDPRLMVVVGPCS 61 Query: 72 LHDPKAAYDYADRLAKISEKLSKDLLIIMRAYLEKPRTTVGWKGLINDPDMNNSFQINKG 131 +HDP+AA +YA+RLA+++++LS L ++MR Y EKPRTT+GWKGLINDPD+N + QI+KG Sbjct: 62 IHDPRAALEYAERLARLNQQLSDQLFLVMRLYFEKPRTTIGWKGLINDPDLNGTHQISKG 121 Query: 132 LRISREMFIKLVE-KLPIAGEMLDTISPQFLSDCFSLGAIGARTTESQLHRELASGLSFP 190 L + R + + E +LP+A EMLD I+P +L+D S GAIGARTTESQ+HRE+ASGLSFP Sbjct: 122 LGVGRSLLCAITELELPVACEMLDPITPHYLADAISWGAIGARTTESQVHREMASGLSFP 181 Query: 191 IGFKNGTDGGLQVAIDAMRAAAHEHYFLSVTKPGVTAIVGTEGNKDTFLILRGGKNGTNF 250 +GFKNGTDG LQ+AIDAM AA H H FL + G AIV T GN D ++LRGG +G NF Sbjct: 182 VGFKNGTDGNLQIAIDAMNAALHPHNFLGIDNDGRNAIVSTAGNSDVHIVLRGGNHGPNF 241 Query: 251 DKESVQNTKKQLEKAGLTDDSQKRIMIDCSHGNSNKDFKNQPKVAKCIYDQLTEGENSLC 310 E ++ T++ L KAGL RIM+DCSH NSNKD + Q V K + +Q+ G S+C Sbjct: 242 QAEDIRGTEEMLGKAGL----PIRIMVDCSHANSNKDHERQEAVLKDVIEQIGAGNRSIC 297 Query: 311 GVMIESNINEGRQDIPKEGGREGLKYGCSVTDACIGWESTEQVL 354 VM+ESN+ G Q ++ + LKYG S+TD CIGW TE++L Sbjct: 298 AVMVESNLEPGNQPTCEDFSK--LKYGVSITDKCIGWADTERML 339 Lambda K H 0.317 0.136 0.400 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: 407 Number of extensions: 13 Number of successful extensions: 4 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: 370 Length of database: 355 Length adjustment: 29 Effective length of query: 341 Effective length of database: 326 Effective search space: 111166 Effective search space used: 111166 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_092058003.1 BQ4888_RS14575 (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.13581.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-155 502.3 0.0 3.1e-155 502.0 0.0 1.0 1 lcl|NCBI__GCF_900111775.1:WP_092058003.1 BQ4888_RS14575 3-deoxy-7-phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900111775.1:WP_092058003.1 BQ4888_RS14575 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 502.0 0.0 3.1e-155 3.1e-155 2 339 .. 6 347 .. 5 349 .. 0.98 Alignments for each domain: == domain 1 score: 502.0 bits; conditional E-value: 3.1e-155 TIGR00034 2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakr 70 +lri + ++++P++lk+ fpl+e+ ae v ++r++i++il+ kd+rl+vv+GPcsihdp+aaleya+r lcl|NCBI__GCF_900111775.1:WP_092058003.1 6 NLRIRRTAPIIAPADLKQVFPLSEHGAEFVYQAREQITNILNHKDPRLMVVVGPCSIHDPRAALEYAER 74 7899***************************************************************** PP TIGR00034 71 lkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatel 139 l++l+++l+d+l +vmr yfekPrtt+GWkGlindPdln+++++ kGl + r ll ++el+lp+a+e+ lcl|NCBI__GCF_900111775.1:WP_092058003.1 75 LARLNQQLSDQLFLVMRLYFEKPRTTIGWKGLINDPDLNGTHQISKGLGVGRSLLCAITELELPVACEM 143 ********************************************************************* PP TIGR00034 140 ldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvt 208 ld+i+p ylad +swgaiGarttesqvhre+asgls+pvgfkngtdG+l++aida++aa ++h fl+++ lcl|NCBI__GCF_900111775.1:WP_092058003.1 144 LDPITPHYLADAISWGAIGARTTESQVHREMASGLSFPVGFKNGTDGNLQIAIDAMNAALHPHNFLGID 212 ********************************************************************* PP TIGR00034 209 kaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276 ++G+ aiv+t+Gn+d hi+lrGG++ pn++aed+ ++e l kagl ++m+d+sh+nsnkd++rq +v lcl|NCBI__GCF_900111775.1:WP_092058003.1 213 NDGRNAIVSTAGNSDVHIVLRGGNHgPNFQAEDIRGTEEMLGKAGLPIRIMVDCSHANSNKDHERQEAV 281 ********************************************************************* PP TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl...keelkyGksvtdacigwedteallrklaeavk 339 ++v+eqi G+++i+ vm+esnle Gnq ++lkyG+s+td+cigw dte++lr ++++k lcl|NCBI__GCF_900111775.1:WP_092058003.1 282 LKDVIEQIGAGNRSICAVMVESNLEPGNQPTcedFSKLKYGVSITDKCIGWADTERMLRYAHQTLK 347 *****************************884334689*********************9888765 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: 10.33 // [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