Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_096777355.1 B076_RS0105120 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_000483485.1:WP_096777355.1 Length = 356 Score = 459 bits (1182), Expect = e-134 Identities = 223/348 (64%), Positives = 273/348 (78%), Gaps = 1/348 (0%) Query: 3 YQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCS 62 YQ DDLRIK I E+ PP L E+FP TE AA TV R+ IH IL G DDRLLV+IGPCS Sbjct: 5 YQTDDLRIKNITEVRPPCELHEQFPITEMAAQTVYDTRQQIHNILSGRDDRLLVIIGPCS 64 Query: 63 IHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDG 122 IHDP AA++YATRL L E+ +++L IVMRVYFEKPRTTVGWKGLINDP ++ SF+IN G Sbjct: 65 IHDPKAARDYATRLKGLIEQHREDLLIVMRVYFEKPRTTVGWKGLINDPGLNESFEINRG 124 Query: 123 LRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCP 182 L +AR LLLD+ND G+PAA EFLD+I+PQY+ADL+SWGAIGARTTESQ HRELASGLSCP Sbjct: 125 LELARSLLLDVNDMGVPAATEFLDLISPQYIADLISWGAIGARTTESQGHRELASGLSCP 184 Query: 183 VGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKE-PNY 241 VGFKN TDG+ ++A+DAI AA PH F+S+TK GHSAI T+GN DCH+ILRGG E PNY Sbjct: 185 VGFKNSTDGSFQIAVDAIRAANNPHIFMSLTKAGHSAIFETNGNPDCHVILRGGNEGPNY 244 Query: 242 SAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMV 301 HV + + L AG+ ++M+D SHANSSKQ ++Q+ V + +Q++ G I+G M+ Sbjct: 245 DEAHVKQAVDMLQTAGVEDKLMVDCSHANSSKQHERQLVVAESIAEQLSNGSPHIMGAMI 304 Query: 302 ESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 ESHLV G Q ++ GEPL YG+SITDACIGWED++ +L+ LA VKARR Sbjct: 305 ESHLVAGRQDVQPGEPLTYGQSITDACIGWEDSEKILQTLAQGVKARR 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: 432 Number of extensions: 16 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_096777355.1 B076_RS0105120 (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.25175.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-170 550.7 0.0 5.7e-170 550.5 0.0 1.0 1 lcl|NCBI__GCF_000483485.1:WP_096777355.1 B076_RS0105120 3-deoxy-7-phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000483485.1:WP_096777355.1 B076_RS0105120 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 550.5 0.0 5.7e-170 5.7e-170 1 342 [] 8 352 .. 8 352 .. 0.99 Alignments for each domain: == domain 1 score: 550.5 bits; conditional E-value: 5.7e-170 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 ddlri++i e+ +P el+++fp+te aa++v ++r++i++il+G+ddrllv+iGPcsihdp+aa +ya+ lcl|NCBI__GCF_000483485.1:WP_096777355.1 8 DDLRIKNITEVRPPCELHEQFPITEMAAQTVYDTRQQIHNILSGRDDRLLVIIGPCSIHDPKAARDYAT 76 79******************************************************************* PP TIGR00034 70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138 rlk l e+ ++dl ivmrvyfekPrttvGWkGlindP lnesf++n+Gl++ar llld++++g+p+ate lcl|NCBI__GCF_000483485.1:WP_096777355.1 77 RLKGLIEQHREDLLIVMRVYFEKPRTTVGWKGLINDPGLNESFEINRGLELARSLLLDVNDMGVPAATE 145 ********************************************************************* PP TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207 +ld ispqy+adl+swgaiGarttesq hrelasgls+pvgfkn+tdGs ++a+dairaa+++h+f+s lcl|NCBI__GCF_000483485.1:WP_096777355.1 146 FLDLISPQYIADLISWGAIGARTTESQGHRELASGLSCPVGFKNSTDGSFQIAVDAIRAANNPHIFMSL 214 ********************************************************************* PP TIGR00034 208 tkaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqle 275 tkaG++ai et+Gn+d+h+ilrGG++ pnyd+++v+++ + l+ ag +++lm+d+sh+ns+k+++rql lcl|NCBI__GCF_000483485.1:WP_096777355.1 215 TKAGHSAIFETNGNPDCHVILRGGNEgPNYDEAHVKQAVDMLQTAGVEDKLMVDCSHANSSKQHERQLV 283 ********************************************************************* PP TIGR00034 276 vaesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342 vaes++eq+++G+ i+G mies+l+ G+q++ +e+l+yG+s+tdacigwed+e++l+ la+ vk+rr lcl|NCBI__GCF_000483485.1:WP_096777355.1 284 VAESIAEQLSNGSPHIMGAMIESHLVAGRQDVqpGEPLTYGQSITDACIGWEDSEKILQTLAQGVKARR 352 ********************************8889******************************996 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: 00:00:00.01 # Mc/sec: 7.11 // [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