Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_041100488.1 SUTH_RS15450 glutamate 5-kinase
Query= BRENDA::P0A7B5 (367 letters) >NCBI__GCF_000828635.1:WP_041100488.1 Length = 371 Score = 296 bits (759), Expect = 5e-85 Identities = 162/366 (44%), Positives = 232/366 (63%), Gaps = 2/366 (0%) Query: 1 MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60 +++++ +VVK+G++++T + L I E RQ A LHA G ++++V+SGAIAAG + L Sbjct: 5 IAEARRVVVKVGSALVTNNGQGLALDFIAECARQIAALHADGRQVLLVSSGAIAAGMQRL 64 Query: 61 GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120 G+ P + Q AAVGQ L Q +E F +G+ Q+LLT D+ DR R+LNAR T Sbjct: 65 GWTTRPHAMHDLQAAAAVGQMGLAQAYESTFLSHGLKAAQILLTHEDLADRTRYLNARST 124 Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180 L+ LLD +VP+INEND V T EIK GDND L AL A L A+ L++LTDQKGLY+ADPR Sbjct: 125 LQTLLDLAVVPIINENDTVVTDEIKFGDNDTLGALVANLVEAEALIILTDQKGLYSADPR 184 Query: 181 SNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPG 240 +P A LI + D A+AG + SG+ GGM TK++AA A ++G T+I +G +P Sbjct: 185 LDPAATLISEGRADDRRFEAMAGGAGSGISKGGMITKVRAAQRAAKSGAHTLIVSGREPD 244 Query: 241 VIGDVMEGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKG 299 + G ++GTL +A +PL RK+W+ AG +T+D GA A L G SLL G Sbjct: 245 SLLAAARGETIGTLLYAAESPLAARKQWLADHLQLAGALTLDAGAQTA-LAGGRSLLAVG 303 Query: 300 IKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAV 359 + V G+F RG + + +GR+IA G+ Y+S RRIAGH +Q+I+A+LGY + Sbjct: 304 VVRVEGDFERGAAVACRSHDGREIARGLINYSSSEARRIAGHGTQDIEALLGYIDSAELI 363 Query: 360 HRDDMI 365 HRD+++ Sbjct: 364 HRDNLV 369 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: 346 Number of extensions: 12 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: 371 Length adjustment: 30 Effective length of query: 337 Effective length of database: 341 Effective search space: 114917 Effective search space used: 114917 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_041100488.1 SUTH_RS15450 (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.15686.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-131 423.2 2.7 5.3e-131 423.0 2.7 1.0 1 lcl|NCBI__GCF_000828635.1:WP_041100488.1 SUTH_RS15450 glutamate 5-kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000828635.1:WP_041100488.1 SUTH_RS15450 glutamate 5-kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 423.0 2.7 5.3e-131 5.3e-131 1 362 [. 9 369 .. 9 370 .. 0.99 Alignments for each domain: == domain 1 score: 423.0 bits; conditional E-value: 5.3e-131 TIGR01027 1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQ 69 +r+VvK+Gs+++t++ + l++ +ae ++q+a+l+++G++v++vsSGa+aaG+++Lg ++rp+ +++ Q lcl|NCBI__GCF_000828635.1:WP_041100488.1 9 RRVVVKVGSALVTNNGQGLALDFIAECARQIAALHADGRQVLLVSSGAIAAGMQRLGWTTRPHAMHDLQ 77 59*************999*************************************************** PP TIGR01027 70 alaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvave 138 a+aaVGQ L ++ye++f ++glk aQiLLt++dl++r+rylNar+tl++ll+l vvpi+NENDtv ++ lcl|NCBI__GCF_000828635.1:WP_041100488.1 78 AAAAVGQMGLAQAYESTFLSHGLKAAQILLTHEDLADRTRYLNARSTLQTLLDLAVVPIINENDTVVTD 146 ********************************************************************* PP TIGR01027 139 eikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGT 207 eikfGDNDtL alva+lveA++L++ltd++gLy+adpr +p A+li+e ++ ++ ++a+ag++gs + lcl|NCBI__GCF_000828635.1:WP_041100488.1 147 EIKFGDNDTLGALVANLVEAEALIILTDQKGLYSADPRLDPAATLISEGRADDRRFEAMAGGAGSGISK 215 ********************************************************************* PP TIGR01027 208 GGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkii 276 GGm tK+ aa+ A+++g +++i+sg++p++++++++++++gtl+ a ++ l +rkqw++ +++ +G+++ lcl|NCBI__GCF_000828635.1:WP_041100488.1 216 GGMITKVRAAQRAAKSGAHTLIVSGREPDSLLAAARGETIGTLLYAAESPLAARKQWLADHLQLAGALT 284 ********************************************************************* PP TIGR01027 277 vdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeied 345 +d+ga++al g+sLl++gvv veg+F+rg +v +++++g+ei++gl nyss+e ++i+g+ +++ie+ lcl|NCBI__GCF_000828635.1:WP_041100488.1 285 LDAGAQTALAG-GRSLLAVGVVRVEGDFERGAAVACRSHDGREIARGLINYSSSEARRIAGHGTQDIEA 352 *********98.********************************************************* PP TIGR01027 346 vLgyekkeevvhrdnlv 362 +Lgy +++e +hrdnlv lcl|NCBI__GCF_000828635.1:WP_041100488.1 353 LLGYIDSAELIHRDNLV 369 ***************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (371 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: 8.62 // [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