Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate Ac3H11_4998 2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha (EC 2.5.1.54)
Query= BRENDA::C3TIE2 (350 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4998 Length = 366 Score = 407 bits (1046), Expect = e-118 Identities = 206/344 (59%), Positives = 249/344 (72%) Query: 6 DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHD 65 DD RIK ++ L+ P L E P + A V +R AI +IL G DDRL+VV+GPCSIHD Sbjct: 20 DDTRIKAVRPLITPALLQEWLPTPDAAQTLVETSRAAISRILHGQDDRLIVVVGPCSIHD 79 Query: 66 PVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRI 125 A +YA +L + L D+L IVMRVYFEKPRTTVGWKG INDPH+D SF IN+GL + Sbjct: 80 HGQAMDYAHQLKVQADALADDLLIVMRVYFEKPRTTVGWKGYINDPHLDGSFAINEGLEL 139 Query: 126 ARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGF 185 AR+LLLD+ GLP EFLD+++PQ+++DL+SWGAIGARTTESQ HR+LASGLSCPVGF Sbjct: 140 ARQLLLDVLALGLPVGTEFLDLLSPQFISDLVSWGAIGARTTESQSHRQLASGLSCPVGF 199 Query: 186 KNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 245 KNGTDG +KVA DAI AA A H F+ +TK G +AI T GN DCH+ILRGGK+PNYSA Sbjct: 200 KNGTDGGVKVASDAIQAASAAHAFMGMTKMGQAAIFETRGNNDCHVILRGGKQPNYSAAD 259 Query: 246 VAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHL 305 V L AGL QVMID SHANSSKQ ++Q+ V DV QQIA G+ I G+M+ESHL Sbjct: 260 VNATCAVLKAAGLREQVMIDVSHANSSKQHQRQITVADDVAQQIAAGDIRITGLMIESHL 319 Query: 306 VEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 EG Q + +G+PL G S+TDACI T +L LA AV+ARR Sbjct: 320 QEGRQDIVAGQPLTPGVSVTDACISLAQTVPVLESLAAAVRARR 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: 396 Number of extensions: 10 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: 366 Length adjustment: 29 Effective length of query: 321 Effective length of database: 337 Effective search space: 108177 Effective search space used: 108177 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 Ac3H11_4998 (2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha (EC 2.5.1.54))
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.18663.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-158 512.6 0.0 2.2e-158 512.4 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4998 2-keto-3-deoxy-D-arabino-heptulo Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4998 2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 512.4 0.0 2.2e-158 2.2e-158 1 342 [] 20 363 .. 20 363 .. 0.99 Alignments for each domain: == domain 1 score: 512.4 bits; conditional E-value: 2.2e-158 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpe 62 dd+ri+++ +l+tP+ l++ p +a++ v++sr +i++il+G+ddrl+vv+GPcsihd lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4998 20 DDTRIKAVRPLITPALLQEWLPTPDAAQTLVETSRAAISRILHGQDDRLIVVVGPCSIHDHG 81 799*********************************************************** PP TIGR00034 63 aaleyakrlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkl 124 a++ya++lk a+ l ddl ivmrvyfekPrttvGWkG indP+l++sf +n+Gl++ar+l lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4998 82 QAMDYAHQLKVQADALADDLLIVMRVYFEKPRTTVGWKGYINDPHLDGSFAINEGLELARQL 143 ************************************************************** PP TIGR00034 125 lldlvelglplatelldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdG 186 lld+ lglp++te+ld spq+++dl+swgaiGarttesq hr+lasgls+pvgfkngtdG lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4998 144 LLDVLALGLPVGTEFLDLLSPQFISDLVSWGAIGARTTESQSHRQLASGLSCPVGFKNGTDG 205 ************************************************************** PP TIGR00034 187 slkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeel 248 ++kva dai+aa+a h f+++tk Gq+ai et+Gn+d+h+ilrGGk+pny+a+dv+++++ l lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4998 206 GVKVASDAIQAASAAHAFMGMTKMGQAAIFETRGNNDCHVILRGGKQPNYSAADVNATCAVL 267 ************************************************************** PP TIGR00034 249 ekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl..k 308 ++agl+e++mid+sh+ns+k+++rq+ va++v++qia G+ i+G+mies+l+eG+q++ + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4998 268 KAAGLREQVMIDVSHANSSKQHQRQITVADDVAQQIAAGDIRITGLMIESHLQEGRQDIvaG 329 **********************************************************9889 PP TIGR00034 309 eelkyGksvtdacigwedteallrklaeavkerr 342 ++l+ G+svtdaci++ +t +l+ la+av++rr lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4998 330 QPLTPGVSVTDACISLAQTVPVLESLAAAVRARR 363 9******************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (366 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 6.70 // [ok]
This GapMind analysis is from Apr 09 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