Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011652224.1 RL_RS13870 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_000009265.1:WP_011652224.1 Length = 353 Score = 417 bits (1071), Expect = e-121 Identities = 209/344 (60%), Positives = 253/344 (73%) Query: 6 DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHD 65 DDLRI EI L P ++ + P + + TV R AIH+IL+G DDRL+VVIGPCSIHD Sbjct: 6 DDLRIVEITPLTKPADIIAEIPRNADVSKTVTSNRDAIHQILRGEDDRLIVVIGPCSIHD 65 Query: 66 PVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRI 125 PVAA++YA RL R+ +LEIVMRVYFEKPRTTVGWKGL+NDPH+D S++I +GLRI Sbjct: 66 PVAARDYAARLTEQRQRFAGDLEIVMRVYFEKPRTTVGWKGLMNDPHLDGSYRIEEGLRI 125 Query: 126 ARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGF 185 AR+LLLDIN GLPA EFLD ITPQY+ADL+SWGAIGARTTESQ+HR+LASGLSCP+GF Sbjct: 126 ARRLLLDINAMGLPAGVEFLDTITPQYIADLVSWGAIGARTTESQIHRQLASGLSCPIGF 185 Query: 186 KNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 245 KNGTDG ++VA+DAI AA PH F +VTK G +AI +T+GN DCHIILRGGK P+Y A Sbjct: 186 KNGTDGGVRVALDAILAASQPHHFPAVTKDGQAAIASTTGNEDCHIILRGGKRPSYEAAD 245 Query: 246 VAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHL 305 V V K G+ +++ID SHANS K Q V V QIA G I G+M+ES+L Sbjct: 246 VEAVTGEAVKLGVAPRILIDASHANSGKDPMNQPLVVKSVAAQIAAGNSDIKGMMIESNL 305 Query: 306 VEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 V G Q L G+PL YG+SITD CI WE + A+L LA + + RR Sbjct: 306 VAGRQDLVPGKPLVYGQSITDGCIDWEMSVAVLEDLAKSARERR 349 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: 418 Number of extensions: 10 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: 353 Length adjustment: 29 Effective length of query: 321 Effective length of database: 324 Effective search space: 104004 Effective search space used: 104004 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_011652224.1 RL_RS13870 (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.13970.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-159 515.7 0.0 2.6e-159 515.5 0.0 1.0 1 lcl|NCBI__GCF_000009265.1:WP_011652224.1 RL_RS13870 3-deoxy-7-phosphohept Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009265.1:WP_011652224.1 RL_RS13870 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 515.5 0.0 2.6e-159 2.6e-159 1 342 [] 6 349 .. 6 349 .. 0.99 Alignments for each domain: == domain 1 score: 515.5 bits; conditional E-value: 2.6e-159 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 ddlriv+i +l+ P++++a++p +++ ++v+++r++i++il+G+ddrl+vviGPcsihdp aa +ya lcl|NCBI__GCF_000009265.1:WP_011652224.1 6 DDLRIVEITPLTKPADIIAEIPRNADVSKTVTSNRDAIHQILRGEDDRLIVVIGPCSIHDPVAARDYAA 74 79******************************************************************* PP TIGR00034 70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138 rl++ ++++ dleivmrvyfekPrttvGWkGl+ndP+l++s+++++Glriar+llld++ +glp++ e lcl|NCBI__GCF_000009265.1:WP_011652224.1 75 RLTEQRQRFAGDLEIVMRVYFEKPRTTVGWKGLMNDPHLDGSYRIEEGLRIARRLLLDINAMGLPAGVE 143 ********************************************************************* PP TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207 +ldti+pqy+adl+swgaiGarttesq+hr+lasgls+p+gfkngtdG+++va+dai aa+++h+f +v lcl|NCBI__GCF_000009265.1:WP_011652224.1 144 FLDTITPQYIADLVSWGAIGARTTESQIHRQLASGLSCPIGFKNGTDGGVRVALDAILAASQPHHFPAV 212 ********************************************************************* PP TIGR00034 208 tkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276 tk+Gq+ai +t+Gned+hiilrGGk+p y+a+dv++v+ e k+g ++++id+sh+ns kd +q+ v lcl|NCBI__GCF_000009265.1:WP_011652224.1 213 TKDGQAAIASTTGNEDCHIILRGGKRPSYEAADVEAVTGEAVKLGVAPRILIDASHANSGKDPMNQPLV 281 ********************************************************************* PP TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342 ++sv++qia G+ i G+miesnl+ G+q+l +++l+yG+s+td ci+we++ a+l++la++ +err lcl|NCBI__GCF_000009265.1:WP_011652224.1 282 VKSVAAQIAAGNSDIKGMMIESNLVAGRQDLvpGKPLVYGQSITDGCIDWEMSVAVLEDLAKSARERR 349 ******************************9899****************************999986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (353 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: 10.14 // [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