Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_024851331.1 N745_RS0106570 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_000526715.1:WP_024851331.1 Length = 355 Score = 446 bits (1146), Expect = e-130 Identities = 220/349 (63%), Positives = 270/349 (77%), Gaps = 1/349 (0%) Query: 2 NYQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPC 61 ++Q DDLRIK I E+ P L EK+P +E AA TV R+AI KIL G+DDR+LVVIGPC Sbjct: 3 HFQTDDLRIKAITEVSAPEKLHEKYPISEAAAQTVYRTREAIKKILNGDDDRMLVVIGPC 62 Query: 62 SIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQIND 121 SIHDP AA++YA RL AL ++ D+L IVMRVYFEKPRTTVGWKGLINDP +D SF+IN Sbjct: 63 SIHDPQAARDYAKRLKALIDKHADDLLIVMRVYFEKPRTTVGWKGLINDPSLDESFEINR 122 Query: 122 GLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSC 181 GL +AR LLLDIN SG+P+A EFLD+I+PQY+ADL+SWGAIGARTTESQ HRELASG+SC Sbjct: 123 GLELARSLLLDINSSGVPSATEFLDLISPQYVADLISWGAIGARTTESQGHRELASGISC 182 Query: 182 PVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKE-PN 240 P+GFKNGTDG K+A+DAI AA PH FLS+TK GHSAI +T+GN DCH+ILRGG + PN Sbjct: 183 PIGFKNGTDGGFKIAVDAIRAANNPHIFLSLTKQGHSAIFSTTGNPDCHVILRGGNDGPN 242 Query: 241 YSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVM 300 Y A HVAE + L A + +++M+D SHANSSKQ K Q+ V + Q++ GE I+G M Sbjct: 243 YDAPHVAEAVQALESAHVQSRLMVDCSHANSSKQHKNQLVVAESIRDQLSAGEANIMGAM 302 Query: 301 VESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 +ESH+ EG Q + G+ L YG+SITDACIGW+D+ L LA V+ RR Sbjct: 303 IESHIEEGRQDVVEGKALTYGQSITDACIGWDDSITALELLAEGVRNRR 351 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: 416 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: 355 Length adjustment: 29 Effective length of query: 321 Effective length of database: 326 Effective search space: 104646 Effective search space used: 104646 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_024851331.1 N745_RS0106570 (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.23685.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-167 542.0 0.0 2.5e-167 541.8 0.0 1.0 1 lcl|NCBI__GCF_000526715.1:WP_024851331.1 N745_RS0106570 3-deoxy-7-phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000526715.1:WP_024851331.1 N745_RS0106570 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 541.8 0.0 2.5e-167 2.5e-167 1 342 [] 7 351 .. 7 351 .. 0.99 Alignments for each domain: == domain 1 score: 541.8 bits; conditional E-value: 2.5e-167 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 ddlri++i e+ +Pe+l++k+p++e+aa++v ++r++i++il+G+ddr+lvviGPcsihdp+aa +yak lcl|NCBI__GCF_000526715.1:WP_024851331.1 7 DDLRIKAITEVSAPEKLHEKYPISEAAAQTVYRTREAIKKILNGDDDRMLVVIGPCSIHDPQAARDYAK 75 799****************************************************************** PP TIGR00034 70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138 rlk+l +k ddl ivmrvyfekPrttvGWkGlindP l+esf++n+Gl++ar llld++ g+p ate lcl|NCBI__GCF_000526715.1:WP_024851331.1 76 RLKALIDKHADDLLIVMRVYFEKPRTTVGWKGLINDPSLDESFEINRGLELARSLLLDINSSGVPSATE 144 ********************************************************************* PP TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207 +ld ispqy+adl+swgaiGarttesq hrelasg+s+p+gfkngtdG+ k+a+dairaa+++h+fls lcl|NCBI__GCF_000526715.1:WP_024851331.1 145 FLDLISPQYVADLISWGAIGARTTESQGHRELASGISCPIGFKNGTDGGFKIAVDAIRAANNPHIFLSL 213 ********************************************************************* PP TIGR00034 208 tkaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqle 275 tk+G++ai +t+Gn+d+h+ilrGG++ pnyda +vae+ + le a +++lm+d+sh+ns+k++k+ql lcl|NCBI__GCF_000526715.1:WP_024851331.1 214 TKQGHSAIFSTTGNPDCHVILRGGNDgPNYDAPHVAEAVQALESAHVQSRLMVDCSHANSSKQHKNQLV 282 ********************************************************************* PP TIGR00034 276 vaesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342 vaes+ +q++ Ge +i+G mies++eeG+q++ +++l+yG+s+tdacigw+d+ + l+ lae v++rr lcl|NCBI__GCF_000526715.1:WP_024851331.1 283 VAESIRDQLSAGEANIMGAMIESHIEEGRQDVveGKALTYGQSITDACIGWDDSITALELLAEGVRNRR 351 *******************************987889*****************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (355 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: 10.26 // [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