Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_010961479.1 MCA_RS11005 glutamate 5-kinase
Query= BRENDA::P0A7B5 (367 letters) >NCBI__GCF_000008325.1:WP_010961479.1 Length = 374 Score = 286 bits (732), Expect = 6e-82 Identities = 151/363 (41%), Positives = 228/363 (62%), Gaps = 1/363 (0%) Query: 4 SQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYP 63 S+ ++VK+G+++LT G + L++ I + V+Q A+L G ++V+V+SG++A G LG+ Sbjct: 10 SRRVIVKIGSALLTAGGKGLDQPAIGQWVQQIAELRQQGIQVVLVSSGSVAEGMSRLGWK 69 Query: 64 ELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRA 123 P + Q A+VGQ L+Q +E LF +G+ Q+LLT D+ +RER+LN+R T+ Sbjct: 70 TRPHRLNELQAAASVGQMGLVQTYESLFKRHGLQTAQILLTHDDLSNRERYLNSRSTILT 129 Query: 124 LLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNP 183 LL+ ++PVINEND V T EI+ GDND L AL A AD L++LTDQ GL+ +P +P Sbjct: 130 LLELGVIPVINENDTVTTEEIRFGDNDTLGALVANAVEADLLIILTDQAGLFERNPSLDP 189 Query: 184 QAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIG 243 A L+ D L + GDS+SGLG GGM TKL+AA +A R+G T+IA+G + GV+ Sbjct: 190 SAPLVPQAGINDPRLNDMVGDSLSGLGRGGMITKLRAARLAARSGTATVIASGRESGVLP 249 Query: 244 DVMEGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKGIKS 302 +++G +GTL +PL RKRW+ G G VDEGA + + G SLLP G+ + Sbjct: 250 RILDGEELGTLLIPDVSPLIARKRWMAGQLKLKGCFVVDEGAARVLRDAGKSLLPIGVIA 309 Query: 303 VTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRD 362 V G F RG+++ + G++IA G++ Y+++ R I S I+ ILGY P +HRD Sbjct: 310 VEGEFRRGDLVACTDSAGQEIARGLTNYSAEEARLIMRQPSTRIEEILGYVDEPELIHRD 369 Query: 363 DMI 365 +++ Sbjct: 370 NLV 372 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: 334 Number of extensions: 13 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: 374 Length adjustment: 30 Effective length of query: 337 Effective length of database: 344 Effective search space: 115928 Effective search space used: 115928 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_010961479.1 MCA_RS11005 (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.25896.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-128 413.7 0.0 4.1e-128 413.5 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010961479.1 MCA_RS11005 glutamate 5-kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010961479.1 MCA_RS11005 glutamate 5-kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 413.5 0.0 4.1e-128 4.1e-128 1 362 [. 11 372 .. 11 373 .. 0.99 Alignments for each domain: == domain 1 score: 413.5 bits; conditional E-value: 4.1e-128 TIGR01027 1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQ 69 +r++vK+Gs++Lt++ + l+++ + + v+q+a+l+++G +vv+vsSG+va G+++Lg ++rp++l+e Q lcl|NCBI__GCF_000008325.1:WP_010961479.1 11 RRVIVKIGSALLTAGGKGLDQPAIGQWVQQIAELRQQGIQVVLVSSGSVAEGMSRLGWKTRPHRLNELQ 79 589****************************************************************** PP TIGR01027 70 alaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvave 138 a+a+VGQ L+++ye+lf+++gl++aQiLLt++dls+rerylN r+t+ +llelgv+p++NENDtv++e lcl|NCBI__GCF_000008325.1:WP_010961479.1 80 AAASVGQMGLVQTYESLFKRHGLQTAQILLTHDDLSNRERYLNSRSTILTLLELGVIPVINENDTVTTE 148 ********************************************************************* PP TIGR01027 139 eikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGT 207 ei+fGDNDtL alva+ veAdlL++ltd+ gL++++p +p A l+++ + l+ + g+s s +G lcl|NCBI__GCF_000008325.1:WP_010961479.1 149 EIRFGDNDTLGALVANAVEADLLIILTDQAGLFERNPSLDPSAPLVPQAGINDPRLNDMVGDSLSGLGR 217 ***************************************************************999*** PP TIGR01027 208 GGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkii 276 GGm tKl aa+lA+r+g ++iasg++ + ++l+++++gtl+ + + l +rk+w++ +++ kG + lcl|NCBI__GCF_000008325.1:WP_010961479.1 218 GGMITKLRAARLAARSGTATVIASGRESGVLPRILDGEELGTLLIPDVSPLIARKRWMAGQLKLKGCFV 286 ********************************************************************* PP TIGR01027 277 vdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeied 345 vdega++ l++ gksLlp gv++veg+F+rg+ v +++ +gqei++gl+nys+ee + i++++s+ ie+ lcl|NCBI__GCF_000008325.1:WP_010961479.1 287 VDEGAARVLRDAGKSLLPIGVIAVEGEFRRGDLVACTDSAGQEIARGLTNYSAEEARLIMRQPSTRIEE 355 ********************************************************************* PP TIGR01027 346 vLgyekkeevvhrdnlv 362 +Lgy ++ e +hrdnlv lcl|NCBI__GCF_000008325.1:WP_010961479.1 356 ILGYVDEPELIHRDNLV 372 ***************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (374 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: 11.11 // [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