Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate HSERO_RS07160 HSERO_RS07160 phospho-2-dehydro-3-deoxyheptonate aldolase
Query= BRENDA::C3TIE2 (350 letters) >FitnessBrowser__HerbieS:HSERO_RS07160 Length = 357 Score = 478 bits (1231), Expect = e-140 Identities = 236/346 (68%), Positives = 282/346 (81%) Query: 4 QNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSI 63 + DDLRI+E+KEL+PP L+ +F TE T A AR A+H+IL G DDRL+VVIGPCSI Sbjct: 3 RTDDLRIREMKELVPPSHLIREFACTEKVERTTAEARTALHRILHGQDDRLMVVIGPCSI 62 Query: 64 HDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGL 123 HD AA EYA RL+ RE K+ELEIVMRVYFEKPRTTVGWKGLINDP+MDNSF+INDGL Sbjct: 63 HDTKAAMEYARRLVVERERHKNELEIVMRVYFEKPRTTVGWKGLINDPYMDNSFRINDGL 122 Query: 124 RIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPV 183 R AR+LLL+IN+ GLPA EFLD+I+PQY+ADL+SWGAIGARTTESQVHRELASGLSCPV Sbjct: 123 RAARELLLNINELGLPAGTEFLDVISPQYIADLISWGAIGARTTESQVHRELASGLSCPV 182 Query: 184 GFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSA 243 GFKNGTDG +K+A+DAI AA PH FLSVTK GHSAIV+T+GN DCHIILRGGK+PNY A Sbjct: 183 GFKNGTDGNVKIAVDAIKAASQPHHFLSVTKGGHSAIVSTAGNEDCHIILRGGKQPNYDA 242 Query: 244 KHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVES 303 V + + K+GL A++MID SHANSSK+ + Q+ VCAD+ +QIAGG+ I+GVMVES Sbjct: 243 PSVEAACQDIAKSGLAARLMIDASHANSSKKPENQIPVCADIGRQIAGGDTRIVGVMVES 302 Query: 304 HLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 HLV G Q L G+ L YG+SITD CI WE++ +L+ LA++VK RR Sbjct: 303 HLVAGRQDLVPGKELTYGQSITDGCINWEESLQVLQGLADSVKQRR 348 Lambda K H 0.317 0.134 0.397 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: 450 Number of extensions: 9 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: 350 Length of database: 357 Length adjustment: 29 Effective length of query: 321 Effective length of database: 328 Effective search space: 105288 Effective search space used: 105288 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: 49 (23.5 bits)
Align candidate HSERO_RS07160 HSERO_RS07160 (phospho-2-dehydro-3-deoxyheptonate aldolase)
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.24605.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-168 543.7 0.0 7.8e-168 543.5 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS07160 HSERO_RS07160 phospho-2-dehydro- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS07160 HSERO_RS07160 phospho-2-dehydro-3-deoxyheptonate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 543.5 0.0 7.8e-168 7.8e-168 1 342 [] 5 348 .. 5 348 .. 0.99 Alignments for each domain: == domain 1 score: 543.5 bits; conditional E-value: 7.8e-168 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleya 68 ddlri +++el++P++l+++f+ tek++ + a++r+++++il+G+ddrl+vviGPcsihd +aa+eya lcl|FitnessBrowser__HerbieS:HSERO_RS07160 5 DDLRIREMKELVPPSHLIREFACTEKVERTTAEARTALHRILHGQDDRLMVVIGPCSIHDTKAAMEYA 72 799***************************************************************** PP TIGR00034 69 krlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglpla 136 +rl +e+ k++leivmrvyfekPrttvGWkGlindP++++sf++n+Glr ar+lll+++elglp++ lcl|FitnessBrowser__HerbieS:HSERO_RS07160 73 RRLVVERERHKNELEIVMRVYFEKPRTTVGWKGLINDPYMDNSFRINDGLRAARELLLNINELGLPAG 140 ******************************************************************** PP TIGR00034 137 telldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlf 204 te+ld+ispqy+adl+swgaiGarttesqvhrelasgls+pvgfkngtdG++k+a+dai+aa+++h+f lcl|FitnessBrowser__HerbieS:HSERO_RS07160 141 TEFLDVISPQYIADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNVKIAVDAIKAASQPHHF 208 ******************************************************************** PP TIGR00034 205 lsvtkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykr 272 lsvtk G++aiv+t+Gned+hiilrGGk+pnyda +v+++++++ k gl ++lmid+sh+ns+k+ ++ lcl|FitnessBrowser__HerbieS:HSERO_RS07160 209 LSVTKGGHSAIVSTAGNEDCHIILRGGKQPNYDAPSVEAACQDIAKSGLAARLMIDASHANSSKKPEN 276 ******************************************************************** PP TIGR00034 273 qlevaesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeav 338 q+ v++++ +qia G++ i+Gvm+es+l+ G+q+l ++el+yG+s+td ci+we++ ++l+ la++v lcl|FitnessBrowser__HerbieS:HSERO_RS07160 277 QIPVCADIGRQIAGGDTRIVGVMVESHLVAGRQDLvpGKELTYGQSITDGCINWEESLQVLQGLADSV 344 **********************************9899****************************** PP TIGR00034 339 kerr 342 k+rr lcl|FitnessBrowser__HerbieS:HSERO_RS07160 345 KQRR 348 *996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (357 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.59 // [ok]
This GapMind analysis is from Apr 09 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