Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_092992403.1 BLP65_RS02755 glutamate 5-kinase
Query= BRENDA::P0A7B5 (367 letters) >NCBI__GCF_900102855.1:WP_092992403.1 Length = 375 Score = 287 bits (734), Expect = 4e-82 Identities = 156/359 (43%), Positives = 215/359 (59%), Gaps = 1/359 (0%) Query: 8 VVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELPA 67 VVK+G+++LT + LN I V Q A L G +V+V+SGA+A G LG+ P Sbjct: 14 VVKIGSALLTDDGKGLNLEGIATWVEQLAALRRQGIEVVLVSSGAVAQGMGRLGWKRRPH 73 Query: 68 TIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLDN 127 + Q AAVGQ L+Q +E F Y +H Q+LLT D+ R R+LNAR TL+ LL Sbjct: 74 ALHELQAAAAVGQMGLVQAYESHFQKYDMHTAQVLLTHDDLSSRGRYLNARSTLKTLLGF 133 Query: 128 NIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNPQAEL 187 +VPV+NEND V T EI+ GDND L AL L A+ L++LTDQ+GL+ DPRSNP A L Sbjct: 134 GVVPVVNENDTVVTDEIRFGDNDTLGALVTNLVEAELLVILTDQEGLFDTDPRSNPDAGL 193 Query: 188 IKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVME 247 + + L +AG LG GGM TKL+AA +A R+G T+IAAG +PG++G + Sbjct: 194 VSEAKANAPELTQMAGGGHGALGRGGMMTKLRAARLAARSGAATVIAAGREPGILGKIFS 253 Query: 248 GISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKGIKSVTGN 306 G SVGTL PL RK+W+ G G + +DEGA + E G SLL G+K V G+ Sbjct: 254 GRSVGTLLLPDKEPLVARKQWLAGHLQMRGRLILDEGACRVLRESGRSLLAVGVKEVVGD 313 Query: 307 FSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMI 365 F+RGE++ + G +IA G+ Y+S+ R+I G S + LG+ P +HRD+++ Sbjct: 314 FARGEMVVCEDENGVEIARGLVNYSSEETRKIRGLPSSRFEETLGFVDEPELIHRDNLV 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: 351 Number of extensions: 14 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: 375 Length adjustment: 30 Effective length of query: 337 Effective length of database: 345 Effective search space: 116265 Effective search space used: 116265 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_092992403.1 BLP65_RS02755 (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.15627.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-132 428.7 0.0 1.1e-132 428.5 0.0 1.0 1 lcl|NCBI__GCF_900102855.1:WP_092992403.1 BLP65_RS02755 glutamate 5-kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900102855.1:WP_092992403.1 BLP65_RS02755 glutamate 5-kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 428.5 0.0 1.1e-132 1.1e-132 2 362 .. 12 372 .. 11 373 .. 0.99 Alignments for each domain: == domain 1 score: 428.5 bits; conditional E-value: 1.1e-132 TIGR01027 2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQa 70 r VvK+Gs++Lt++ + l+++ +a+ veq+a+l+++G evv+vsSGava G+ +Lg ++rp+ l+e Qa lcl|NCBI__GCF_900102855.1:WP_092992403.1 12 RWVVKIGSALLTDDGKGLNLEGIATWVEQLAALRRQGIEVVLVSSGAVAQGMGRLGWKRRPHALHELQA 80 67******************************************************************* PP TIGR01027 71 laaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvavee 139 +aaVGQ L+++ye+ f++y++++aQ+LLt++dls+r rylNar+tl++ll +gvvp+vNENDtv ++e lcl|NCBI__GCF_900102855.1:WP_092992403.1 81 AAAVGQMGLVQAYESHFQKYDMHTAQVLLTHDDLSSRGRYLNARSTLKTLLGFGVVPVVNENDTVVTDE 149 ********************************************************************* PP TIGR01027 140 ikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTG 208 i+fGDNDtL alv++lveA+lLv+ltd++gL+d+dpr+npdA l++e ++ + el+++ag++ ++G G lcl|NCBI__GCF_900102855.1:WP_092992403.1 150 IRFGDNDTLGALVTNLVEAELLVILTDQEGLFDTDPRSNPDAGLVSEAKANAPELTQMAGGGHGALGRG 218 *************************************************************9999**** PP TIGR01027 209 GmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiiv 277 Gm+tKl aa+lA+r+g ++ia+g++p + ++ ++++vgtl+ + k+ l +rkqw++ +++ +G++i+ lcl|NCBI__GCF_900102855.1:WP_092992403.1 219 GMMTKLRAARLAARSGAATVIAAGREPGILGKIFSGRSVGTLLLPDKEPLVARKQWLAGHLQMRGRLIL 287 ********************************************************************* PP TIGR01027 278 degaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeiedv 346 dega + l+e g+sLl++gv ev g+F rge+v + +e+g ei++glvnyssee +ki gl+s+ e+ lcl|NCBI__GCF_900102855.1:WP_092992403.1 288 DEGACRVLRESGRSLLAVGVKEVVGDFARGEMVVCEDENGVEIARGLVNYSSEETRKIRGLPSSRFEET 356 ********************************************************************* PP TIGR01027 347 Lgyekkeevvhrdnlv 362 Lg+ ++ e +hrdnlv lcl|NCBI__GCF_900102855.1:WP_092992403.1 357 LGFVDEPELIHRDNLV 372 **************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (375 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: 7.89 // [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