Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_013516945.1 ALIDE2_RS00135 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_000204645.1:WP_013516945.1 Length = 367 Score = 412 bits (1059), Expect = e-120 Identities = 210/344 (61%), Positives = 251/344 (72%) Query: 6 DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHD 65 DDLRIK ++ L+ P L E PA++ A V +R I ++L G DDRL+VV+GPCSIHD Sbjct: 20 DDLRIKAVRPLITPAILEEWLPASDAAQALVEESRLQISRVLHGQDDRLIVVVGPCSIHD 79 Query: 66 PVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRI 125 A EYA +LLA L +L IVMRVYFEKPRTTVGWKG INDPH+D SF IN+GL Sbjct: 80 HDQAMEYARQLLAQARALAQDLLIVMRVYFEKPRTTVGWKGYINDPHLDGSFAINEGLER 139 Query: 126 ARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGF 185 AR LLLDI GLP EFLD+++PQ+++DL+SWGAIGARTTESQ HR+LASGLSCPVGF Sbjct: 140 ARALLLDILALGLPVGTEFLDLLSPQFISDLVSWGAIGARTTESQSHRQLASGLSCPVGF 199 Query: 186 KNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 245 KNGTDG +KVA DAI AA APH F+ +TK G +AI T GN DCH+ILRGGK PNY A Sbjct: 200 KNGTDGGVKVAADAIQAAQAPHAFMGMTKMGQAAIFETRGNRDCHVILRGGKAPNYGAAD 259 Query: 246 VAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHL 305 V + L KAG AQVMID SHANSSKQ +Q+ V A+V +QIA G+ I GVM+ESHL Sbjct: 260 VQAACDLLEKAGQRAQVMIDLSHANSSKQHARQITVAAEVARQIAAGDARITGVMIESHL 319 Query: 306 VEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 EG Q + G+ L +G S+TDACI + T +L QLA AV+ARR Sbjct: 320 EEGRQDIVPGQALRHGVSVTDACISFAQTVPVLEQLAAAVRARR 363 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: 373 Number of extensions: 11 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: 367 Length adjustment: 29 Effective length of query: 321 Effective length of database: 338 Effective search space: 108498 Effective search space used: 108498 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_013516945.1 ALIDE2_RS00135 (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.14182.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-158 513.4 0.0 1.3e-158 513.2 0.0 1.0 1 lcl|NCBI__GCF_000204645.1:WP_013516945.1 ALIDE2_RS00135 3-deoxy-7-phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204645.1:WP_013516945.1 ALIDE2_RS00135 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 513.2 0.0 1.3e-158 1.3e-158 1 342 [] 20 363 .. 20 363 .. 0.99 Alignments for each domain: == domain 1 score: 513.2 bits; conditional E-value: 1.3e-158 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 ddlri+++ +l+tP+ l++ p++ +a++ v++sr +i+++l+G+ddrl+vv+GPcsihd a+eya+ lcl|NCBI__GCF_000204645.1:WP_013516945.1 20 DDLRIKAVRPLITPAILEEWLPASDAAQALVEESRLQISRVLHGQDDRLIVVVGPCSIHDHDQAMEYAR 88 799****************************************************************** PP TIGR00034 70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138 +l + a l +dl ivmrvyfekPrttvGWkG indP+l++sf +n+Gl+ ar llld+ lglp++te lcl|NCBI__GCF_000204645.1:WP_013516945.1 89 QLLAQARALAQDLLIVMRVYFEKPRTTVGWKGYINDPHLDGSFAINEGLERARALLLDILALGLPVGTE 157 ********************************************************************* PP TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207 +ld spq+++dl+swgaiGarttesq hr+lasgls+pvgfkngtdG++kva dai+aa+a+h f+++ lcl|NCBI__GCF_000204645.1:WP_013516945.1 158 FLDLLSPQFISDLVSWGAIGARTTESQSHRQLASGLSCPVGFKNGTDGGVKVAADAIQAAQAPHAFMGM 226 ********************************************************************* PP TIGR00034 208 tkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276 tk Gq+ai et+Gn+d+h+ilrGGk+pny a+dv+++++ lekag+++++mid+sh+ns+k++ rq+ v lcl|NCBI__GCF_000204645.1:WP_013516945.1 227 TKMGQAAIFETRGNRDCHVILRGGKAPNYGAADVQAACDLLEKAGQRAQVMIDLSHANSSKQHARQITV 295 ********************************************************************* PP TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342 a++v++qia G+ i+Gvmies+leeG+q++ +++l +G+svtdaci++ +t +l++la+av++rr lcl|NCBI__GCF_000204645.1:WP_013516945.1 296 AAEVARQIAAGDARITGVMIESHLEEGRQDIvpGQALRHGVSVTDACISFAQTVPVLEQLAAAVRARR 363 *******************************999*******************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (367 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: 7.17 // [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