Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_014146675.1 MEALZ_RS00825 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_000968535.2:WP_014146675.1 Length = 356 Score = 455 bits (1170), Expect = e-133 Identities = 231/348 (66%), Positives = 275/348 (79%), Gaps = 1/348 (0%) Query: 3 YQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCS 62 Y DDLRI E KE++ PVA+ E+ P E AA TV R IH IL G+DDRLLVVIGPCS Sbjct: 5 YNTDDLRISETKEVIAPVAVHEELPMNELAATTVLQTRAEIHDILTGDDDRLLVVIGPCS 64 Query: 63 IHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDG 122 IH+P AA EY RL +++EL +L IVMRVYFEKPRTTVGWKGLINDP +D+SF IN G Sbjct: 65 IHNPEAAIEYGKRLKTIKDELNKDLLIVMRVYFEKPRTTVGWKGLINDPDLDSSFDINKG 124 Query: 123 LRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCP 182 LRIAR+LLLD+N G+PAA E+LD+ITPQY++DL+SWGAIGARTTESQVHRELASGLSC Sbjct: 125 LRIARRLLLDLNTLGMPAATEYLDLITPQYVSDLISWGAIGARTTESQVHRELASGLSCA 184 Query: 183 VGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGK-EPNY 241 VGFKN TDG+IK+AIDAI AA +PH FLS+TK G SAI +T GN D HIILRGG +PNY Sbjct: 185 VGFKNATDGSIKIAIDAIGAAMSPHHFLSLTKEGRSAIFSTRGNEDAHIILRGGNGQPNY 244 Query: 242 SAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMV 301 A +V +V EGL +GL ++MIDFSHANS KQ+++Q+ V DV QIAGG+K IIGVM+ Sbjct: 245 DAVNVEKVAEGLENSGLRPRIMIDFSHANSLKQYQRQLIVGEDVGGQIAGGDKRIIGVMI 304 Query: 302 ESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 ESHL G Q + G+PL +G+SITDAC+GWED+ LL+ LA AV ARR Sbjct: 305 ESHLKAGRQDVIPGKPLTFGQSITDACLGWEDSAQLLKDLAAAVVARR 352 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: 443 Number of extensions: 13 Number of successful extensions: 2 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: 356 Length adjustment: 29 Effective length of query: 321 Effective length of database: 327 Effective search space: 104967 Effective search space used: 104967 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_014146675.1 MEALZ_RS00825 (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.6695.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-164 531.6 0.0 3.8e-164 531.4 0.0 1.0 1 lcl|NCBI__GCF_000968535.2:WP_014146675.1 MEALZ_RS00825 3-deoxy-7-phosphoh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000968535.2:WP_014146675.1 MEALZ_RS00825 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 531.4 0.0 3.8e-164 3.8e-164 1 342 [] 8 352 .. 8 352 .. 0.99 Alignments for each domain: == domain 1 score: 531.4 bits; conditional E-value: 3.8e-164 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 ddlri + +e+++P +++++ p+ e aa++v ++r ei+dil+G+ddrllvviGPcsih+peaa+ey k lcl|NCBI__GCF_000968535.2:WP_014146675.1 8 DDLRISETKEVIAPVAVHEELPMNELAATTVLQTRAEIHDILTGDDDRLLVVIGPCSIHNPEAAIEYGK 76 799****************************************************************** PP TIGR00034 70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138 rlk+++++l++dl ivmrvyfekPrttvGWkGlindPdl+ sfd+nkGlriar+llldl+ lg+p+ate lcl|NCBI__GCF_000968535.2:WP_014146675.1 77 RLKTIKDELNKDLLIVMRVYFEKPRTTVGWKGLINDPDLDSSFDINKGLRIARRLLLDLNTLGMPAATE 145 ********************************************************************* PP TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207 +ld i+pqy++dl+swgaiGarttesqvhrelasgls++vgfkn+tdGs+k+aidai aa ++h+fls lcl|NCBI__GCF_000968535.2:WP_014146675.1 146 YLDLITPQYVSDLISWGAIGARTTESQVHRELASGLSCAVGFKNATDGSIKIAIDAIGAAMSPHHFLSL 214 ********************************************************************* PP TIGR00034 208 tkaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqle 275 tk+G++ai +t+Gned+hiilrGG+ pnyda +v++v e le+ gl++++midfsh+ns k+y+rql lcl|NCBI__GCF_000968535.2:WP_014146675.1 215 TKEGRSAIFSTRGNEDAHIILRGGNGqPNYDAVNVEKVAEGLENSGLRPRIMIDFSHANSLKQYQRQLI 283 ************************988****************************************** PP TIGR00034 276 vaesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342 v e+v qia G+k iiGvmies+l+ G+q++ +++l++G+s+tdac+gwed+ +ll++la+av +rr lcl|NCBI__GCF_000968535.2:WP_014146675.1 284 VGEDVGGQIAGGDKRIIGVMIESHLKAGRQDVipGKPLTFGQSITDACLGWEDSAQLLKDLAAAVVARR 352 *******************************9999******************************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (356 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: 00:00:00.00 # Mc/sec: 12.19 // [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