Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate BPHYT_RS17110 BPHYT_RS17110 glutamate 5-kinase
Query= BRENDA::P0A7B5 (367 letters) >FitnessBrowser__BFirm:BPHYT_RS17110 Length = 372 Score = 287 bits (734), Expect = 4e-82 Identities = 160/366 (43%), Positives = 225/366 (61%), Gaps = 1/366 (0%) Query: 1 MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60 ++DS+ LVVK+G+S++T R L+ A I Q A L A G +V+V+SGAIA G + L Sbjct: 5 IADSRRLVVKVGSSLVTNDGRGLDHAAIGRWAAQIAALRAQGKEVVLVSSGAIAEGMQRL 64 Query: 61 GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120 G+ + P I Q AAVGQ L Q++E F+ + I Q+LLT AD+ DRER+LNAR T Sbjct: 65 GWTKRPREIDELQAAAAVGQMGLAQVYESRFAEHSIQTAQILLTHADLADRERYLNARST 124 Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180 L LL +VP+INEND V T EIK GDND L AL A L D L++LTDQ+GL+TADPR Sbjct: 125 LLTLLRLGVVPIINENDTVVTDEIKFGDNDTLGALVANLIEGDALVILTDQQGLFTADPR 184 Query: 181 SNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPG 240 + A L++ L A+AG + S LG GGM TK+ AA A +G +T+IA+G + Sbjct: 185 KDLTATLVQQADAGALELEAMAGGAGSSLGRGGMLTKILAAKRAAHSGANTVIASGREAD 244 Query: 241 VIGDVMEGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKG 299 V+ + G ++GT A+ + RK+W+ G + +D+GA + E G SLLP G Sbjct: 245 VLSRLASGEAIGTQLIARTARMAARKQWMADHLQVRGHVVIDDGAVEKLTEGGKSLLPIG 304 Query: 300 IKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAV 359 I V G F+RGEVI + GR++A G++ Y+S + I S EI+++LGY P + Sbjct: 305 IVGVQGAFARGEVIACLSAAGREVARGLTNYSSAETKLIQRRPSGEIESVLGYMLEPELI 364 Query: 360 HRDDMI 365 HRD+++ Sbjct: 365 HRDNLV 370 Lambda K H 0.318 0.135 0.384 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: 357 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: 367 Length of database: 372 Length adjustment: 30 Effective length of query: 337 Effective length of database: 342 Effective search space: 115254 Effective search space used: 115254 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 BPHYT_RS17110 BPHYT_RS17110 (glutamate 5-kinase)
to HMM TIGR01027 (proB: glutamate 5-kinase (EC 2.7.2.11))
# 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/TIGR01027.hmm # target sequence database: /tmp/gapView.16592.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01027 [M=363] Accession: TIGR01027 Description: proB: glutamate 5-kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-132 427.3 4.8 3e-132 427.1 4.8 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS17110 BPHYT_RS17110 glutamate 5-kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS17110 BPHYT_RS17110 glutamate 5-kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 427.1 4.8 3e-132 3e-132 1 362 [. 9 370 .. 9 371 .. 0.99 Alignments for each domain: == domain 1 score: 427.1 bits; conditional E-value: 3e-132 TIGR01027 1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQa 70 +r+VvK+Gss++t++ + l+++ + + ++q+a+l+++G+evv+vsSGa+a G+++Lg ++rp+++ e Qa lcl|FitnessBrowser__BFirm:BPHYT_RS17110 9 RRLVVKVGSSLVTNDGRGLDHAAIGRWAAQIAALRAQGKEVVLVSSGAIAEGMQRLGWTKRPREIDELQA 78 589******************************************************************* PP TIGR01027 71 laaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveei 140 +aaVGQ L + ye+ f+++++++aQiLLt+adl++rerylNar+tl +ll lgvvpi+NENDtv ++ei lcl|FitnessBrowser__BFirm:BPHYT_RS17110 79 AAAVGQMGLAQVYESRFAEHSIQTAQILLTHADLADRERYLNARSTLLTLLRLGVVPIINENDTVVTDEI 148 ********************************************************************** PP TIGR01027 141 kfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGm 210 kfGDNDtL alva+l+e d+Lv+ltd++gL++adpr++ +A+l+++ ++ + el+a+ag++gss+G GGm lcl|FitnessBrowser__BFirm:BPHYT_RS17110 149 KFGDNDTLGALVANLIEGDALVILTDQQGLFTADPRKDLTATLVQQADAGALELEAMAGGAGSSLGRGGM 218 ********************************************************************** PP TIGR01027 211 rtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdeg 280 tK+ aa+ A+++g +++iasg++ + + +l++++a+gt++ a+++++ +rkqw++ +++ +G++++d+g lcl|FitnessBrowser__BFirm:BPHYT_RS17110 219 LTKILAAKRAAHSGANTVIASGREADVLSRLASGEAIGTQLIARTARMAARKQWMADHLQVRGHVVIDDG 288 ********************************************************************** PP TIGR01027 281 aeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeiedvLgye 350 a+e+l+e gksLlp g+v+v+g F rgev+ +l+ +g+e+++gl+nyss+e + i++++s eie vLgy lcl|FitnessBrowser__BFirm:BPHYT_RS17110 289 AVEKLTEGGKSLLPIGIVGVQGAFARGEVIACLSAAGREVARGLTNYSSAETKLIQRRPSGEIESVLGYM 358 ********************************************************************** PP TIGR01027 351 kkeevvhrdnlv 362 + e +hrdnlv lcl|FitnessBrowser__BFirm:BPHYT_RS17110 359 LEPELIHRDNLV 370 **********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (372 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: 10.77 // [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