Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate H281DRAFT_04687 H281DRAFT_04687 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
Query= BRENDA::C3TIE2 (350 letters) >FitnessBrowser__Burk376:H281DRAFT_04687 Length = 357 Score = 469 bits (1207), Expect = e-137 Identities = 227/347 (65%), Positives = 280/347 (80%) Query: 3 YQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCS 62 + DD+RI+E+KEL PP L+ +F E ++ + ++R A+H+IL G DDRL+V++GPCS Sbjct: 4 HNTDDVRIRELKELTPPAHLIREFACDEAVSDLIYNSRTAMHRILHGMDDRLIVIVGPCS 63 Query: 63 IHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDG 122 IHD AA EYA RL+ R+ ELE+VMRVYFEKPRTTVGWKGLINDPHMDNSF+IN+G Sbjct: 64 IHDTKAALEYAGRLVEQRKRFAGELEVVMRVYFEKPRTTVGWKGLINDPHMDNSFKINEG 123 Query: 123 LRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCP 182 LR AR+LLL IN+ GLPAA E+LDMI+PQY+ADL+SWGAIGARTTESQVHRELASGLSCP Sbjct: 124 LRTARELLLRINELGLPAATEYLDMISPQYIADLISWGAIGARTTESQVHRELASGLSCP 183 Query: 183 VGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYS 242 VGFKNGTDG +K+A+DAI AA PH FLSVTK GHSAIV+T+GN DCHIILRGGK PNY Sbjct: 184 VGFKNGTDGNVKIAVDAIKAASQPHHFLSVTKGGHSAIVSTAGNEDCHIILRGGKTPNYD 243 Query: 243 AKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVE 302 A V + K+GL A++MID SHANSSK+ + Q+ VCAD+ +Q+A G++ IIGVM+E Sbjct: 244 ADSVNAACSDIGKSGLAARLMIDASHANSSKKHENQIPVCADIGRQVASGDERIIGVMLE 303 Query: 303 SHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 SHLV G Q L+ G L YG+S+TDACIGW+++ A+L LA+AVK RR Sbjct: 304 SHLVAGRQDLQEGCALTYGQSVTDACIGWDESVAVLEGLADAVKQRR 350 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: 461 Number of extensions: 10 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 H281DRAFT_04687 H281DRAFT_04687 (3-deoxy-D-arabinoheptulosonate-7-phosphate 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.15332.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-167 540.6 0.0 6.6e-167 540.4 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04687 H281DRAFT_04687 3-deoxy-D-arabin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04687 H281DRAFT_04687 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 540.4 0.0 6.6e-167 6.6e-167 1 342 [] 7 350 .. 7 350 .. 0.99 Alignments for each domain: == domain 1 score: 540.4 bits; conditional E-value: 6.6e-167 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaale 66 dd+ri +++el++P++l+++f+ e++ + + +sr+++++il+G ddrl+v++GPcsihd +aale lcl|FitnessBrowser__Burk376:H281DRAFT_04687 7 DDVRIRELKELTPPAHLIREFACDEAVSDLIYNSRTAMHRILHGMDDRLIVIVGPCSIHDTKAALE 72 799*************************************************************** PP TIGR00034 67 yakrlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelg 132 ya rl + ++++ +le+vmrvyfekPrttvGWkGlindP++++sf++n+Glr ar+lll ++elg lcl|FitnessBrowser__Burk376:H281DRAFT_04687 73 YAGRLVEQRKRFAGELEVVMRVYFEKPRTTVGWKGLINDPHMDNSFKINEGLRTARELLLRINELG 138 ****************************************************************** PP TIGR00034 133 lplatelldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaa 198 lp+ate+ld+ispqy+adl+swgaiGarttesqvhrelasgls+pvgfkngtdG++k+a+dai+aa lcl|FitnessBrowser__Burk376:H281DRAFT_04687 139 LPAATEYLDMISPQYIADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNVKIAVDAIKAA 204 ****************************************************************** PP TIGR00034 199 aaehlflsvtkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshg 264 +++h+flsvtk G++aiv+t+Gned+hiilrGGk+pnyda++v+++++++ k gl ++lmid+sh+ lcl|FitnessBrowser__Burk376:H281DRAFT_04687 205 SQPHHFLSVTKGGHSAIVSTAGNEDCHIILRGGKTPNYDADSVNAACSDIGKSGLAARLMIDASHA 270 ****************************************************************** PP TIGR00034 265 nsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqslke..elkyGksvtdacigwedte 328 ns+k++++q+ v++++ +q+a+G++ iiGvm+es+l+ G+q+l+e +l+yG+svtdacigw+++ lcl|FitnessBrowser__Burk376:H281DRAFT_04687 271 NSSKKHENQIPVCADIGRQVASGDERIIGVMLESHLVAGRQDLQEgcALTYGQSVTDACIGWDESV 336 *******************************************7622699**************** PP TIGR00034 329 allrklaeavkerr 342 a+l+ la+avk+rr lcl|FitnessBrowser__Burk376:H281DRAFT_04687 337 AVLEGLADAVKQRR 350 ***********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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.84 // [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