Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011766514.1 AZO_RS14015 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_000061505.1:WP_011766514.1 Length = 361 Score = 468 bits (1203), Expect = e-136 Identities = 236/349 (67%), Positives = 273/349 (78%) Query: 1 MNYQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGP 60 M DD+RIKEIKEL+PP +L +FPAT +A T AR+AIH+IL G DDRLLVV+GP Sbjct: 5 MKIHIDDVRIKEIKELVPPAHVLREFPATAKSAETAYEARQAIHRILYGADDRLLVVVGP 64 Query: 61 CSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQIN 120 CSIHD AA EYA RL E LK++L +VMRVYFEKPRTTVGWKGLINDPH+D SF IN Sbjct: 65 CSIHDADAAMEYARRLKVEAERLKNDLLVVMRVYFEKPRTTVGWKGLINDPHLDGSFAIN 124 Query: 121 DGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLS 180 +G+R+ARKLL +IN+ GLPA EFLDMITPQY+ADL+SWGAIGARTTESQVHRELASGLS Sbjct: 125 EGVRLARKLLWEINELGLPAGTEFLDMITPQYIADLISWGAIGARTTESQVHRELASGLS 184 Query: 181 CPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPN 240 CPVGFKNGTDG +++A+DAI AA +PH FLSVTK GHSAIV+T GN DCH ILRGGK N Sbjct: 185 CPVGFKNGTDGNVRIAVDAIKAAQSPHHFLSVTKAGHSAIVSTRGNEDCHAILRGGKSTN 244 Query: 241 YSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVM 300 Y A V + L +G+P +VMIDFSHANS KQ + Q++V DV Q+A GE IIGVM Sbjct: 245 YDAASVDAACKELAASGVPGKVMIDFSHANSRKQHRLQIEVAHDVAAQLARGEDRIIGVM 304 Query: 301 VESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 VESHL EG Q L+ G L YG SITDACIGWED+ +L LA AV+ RR Sbjct: 305 VESHLKEGRQDLKPGCTLEYGMSITDACIGWEDSVGVLDTLAGAVRQRR 353 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: 432 Number of extensions: 7 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: 361 Length adjustment: 29 Effective length of query: 321 Effective length of database: 332 Effective search space: 106572 Effective search space used: 106572 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 WP_011766514.1 AZO_RS14015 (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.25967.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-169 549.0 0.0 1.8e-169 548.9 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011766514.1 AZO_RS14015 3-deoxy-7-phosphohep Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011766514.1 AZO_RS14015 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 548.9 0.0 1.8e-169 1.8e-169 1 342 [] 10 353 .. 10 353 .. 0.99 Alignments for each domain: == domain 1 score: 548.9 bits; conditional E-value: 1.8e-169 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 dd+ri++i+el++P+++ ++fp+t+k+ae+ ++r++i++il G ddrllvv+GPcsihd aa+eya+ lcl|NCBI__GCF_000061505.1:WP_011766514.1 10 DDVRIKEIKELVPPAHVLREFPATAKSAETAYEARQAIHRILYGADDRLLVVVGPCSIHDADAAMEYAR 78 799****************************************************************** PP TIGR00034 70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138 rlk ae+lk+dl +vmrvyfekPrttvGWkGlindP+l++sf +n+G+r+arkll +++elglp++te lcl|NCBI__GCF_000061505.1:WP_011766514.1 79 RLKVEAERLKNDLLVVMRVYFEKPRTTVGWKGLINDPHLDGSFAINEGVRLARKLLWEINELGLPAGTE 147 ********************************************************************* PP TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207 +ld+i+pqy+adl+swgaiGarttesqvhrelasgls+pvgfkngtdG++++a+dai+aa+++h+flsv lcl|NCBI__GCF_000061505.1:WP_011766514.1 148 FLDMITPQYIADLISWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNVRIAVDAIKAAQSPHHFLSV 216 ********************************************************************* PP TIGR00034 208 tkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276 tkaG++aiv+t+Gned+h ilrGGk++nyda++v+++++el + g ++midfsh+ns+k+++ q+ev lcl|NCBI__GCF_000061505.1:WP_011766514.1 217 TKAGHSAIVSTRGNEDCHAILRGGKSTNYDAASVDAACKELAASGVPGKVMIDFSHANSRKQHRLQIEV 285 ********************************************************************* PP TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342 a++v++q+a+Ge+ iiGvm+es+l+eG+q+l + +l+yG+s+tdacigwed+ +l la av++rr lcl|NCBI__GCF_000061505.1:WP_011766514.1 286 AHDVAAQLARGEDRIIGVMVESHLKEGRQDLkpGCTLEYGMSITDACIGWEDSVGVLDTLAGAVRQRR 353 *******************************5556799***************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (361 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.06 // [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