Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_027457786.1 K420_RS0109095 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_000519045.1:WP_027457786.1 Length = 363 Score = 467 bits (1202), Expect = e-136 Identities = 224/344 (65%), Positives = 278/344 (80%) Query: 6 DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHD 65 DD+RI+EIKEL+PP + ++P + AA T +AR+AIH++L G DDRLLVVIGPCSIHD Sbjct: 14 DDVRIREIKELVPPAHVFREYPLSNRAAQTTYNARQAIHRVLHGADDRLLVVIGPCSIHD 73 Query: 66 PVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRI 125 A +YA +L E+ +D+L +VMRVYFEKPRTTVGWKGLINDP +DN+F+IN+GLR+ Sbjct: 74 YDVAMDYAKKLAREAEKYQDDLIVVMRVYFEKPRTTVGWKGLINDPRLDNTFRINEGLRL 133 Query: 126 ARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGF 185 AR++LL+IN+ LP A EFLD ITPQY ADL++WGAIGARTTESQVHRELASGLSCPVGF Sbjct: 134 ARRILLEINELDLPCATEFLDTITPQYTADLIAWGAIGARTTESQVHRELASGLSCPVGF 193 Query: 186 KNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 245 KNGTDG +++A+DAI AA +PH FLSVTK GH+AIV+T GN DCH+ILRGGKEPN+ A Sbjct: 194 KNGTDGNMRIAVDAIRAANSPHHFLSVTKSGHTAIVSTMGNEDCHVILRGGKEPNFDAAS 253 Query: 246 VAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHL 305 V + + KAGL A++M+DFSH NS KQ+K QM+VC V Q+A G++ I+GVMVESHL Sbjct: 254 VEAASQEVAKAGLAARLMVDFSHGNSRKQYKLQMEVCDSVADQLAAGDERIVGVMVESHL 313 Query: 306 VEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 VEG Q L +PL YG+SITDACIGWED+ +L +LA AV+ARR Sbjct: 314 VEGRQDLSPDKPLTYGQSITDACIGWEDSMVVLDRLAAAVRARR 357 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: 442 Number of extensions: 8 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: 363 Length adjustment: 29 Effective length of query: 321 Effective length of database: 334 Effective search space: 107214 Effective search space used: 107214 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_027457786.1 K420_RS0109095 (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.22630.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-170 552.1 0.0 2.1e-170 551.9 0.0 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027457786.1 K420_RS0109095 3-deoxy-7-phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027457786.1 K420_RS0109095 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 551.9 0.0 2.1e-170 2.1e-170 1 342 [] 14 357 .. 14 357 .. 0.99 Alignments for each domain: == domain 1 score: 551.9 bits; conditional E-value: 2.1e-170 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 dd+ri +i+el++P+++ +++pl+++aa++ ++r++i+++l+G ddrllvviGPcsihd a++yak lcl|NCBI__GCF_000519045.1:WP_027457786.1 14 DDVRIREIKELVPPAHVFREYPLSNRAAQTTYNARQAIHRVLHGADDRLLVVIGPCSIHDYDVAMDYAK 82 799****************************************************************** PP TIGR00034 70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138 +l++ aek++ddl +vmrvyfekPrttvGWkGlindP l+++f++n+Glr+ar++ll+++el+lp ate lcl|NCBI__GCF_000519045.1:WP_027457786.1 83 KLAREAEKYQDDLIVVMRVYFEKPRTTVGWKGLINDPRLDNTFRINEGLRLARRILLEINELDLPCATE 151 ********************************************************************* PP TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207 +ldti+pqy adl++wgaiGarttesqvhrelasgls+pvgfkngtdG++++a+dairaa+++h+flsv lcl|NCBI__GCF_000519045.1:WP_027457786.1 152 FLDTITPQYTADLIAWGAIGARTTESQVHRELASGLSCPVGFKNGTDGNMRIAVDAIRAANSPHHFLSV 220 ********************************************************************* PP TIGR00034 208 tkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276 tk+G++aiv+t Gned+h+ilrGGk+pn+da++v+++ +e+ kagl ++lm+dfshgns+k+yk q+ev lcl|NCBI__GCF_000519045.1:WP_027457786.1 221 TKSGHTAIVSTMGNEDCHVILRGGKEPNFDAASVEAASQEVAKAGLAARLMVDFSHGNSRKQYKLQMEV 289 ********************************************************************* PP TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342 ++sv++q+a G++ i+Gvm+es+l+eG+q+l +++l+yG+s+tdacigwed+ +l +la+av++rr lcl|NCBI__GCF_000519045.1:WP_027457786.1 290 CDSVADQLAAGDERIVGVMVESHLVEGRQDLspDKPLTYGQSITDACIGWEDSMVVLDRLAAAVRARR 357 ******************************98889******************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (363 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: 11.84 // [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