Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate GFF4601 PS417_23545 gamma-glutamyl kinase
Query= BRENDA::P0A7B5 (367 letters) >FitnessBrowser__WCS417:GFF4601 Length = 372 Score = 297 bits (760), Expect = 4e-85 Identities = 160/366 (43%), Positives = 230/366 (62%), Gaps = 1/366 (0%) Query: 1 MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60 ++ +Q VVK+G+++LT + L+RA + V Q LH AG +V+V+SGA+AAG L Sbjct: 5 VTGAQRWVVKIGSALLTADGKGLDRAAMSVWVEQMVALHEAGVELVLVSSGAVAAGMSRL 64 Query: 61 GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120 G+ P+ + Q AA+GQ L+Q WE F+ +G H Q+LLT D+ DR+R+LNAR T Sbjct: 65 GWTARPSAMHELQAAAAIGQMGLVQAWESSFADHGRHTAQILLTHDDLSDRKRYLNARST 124 Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180 LRAL++ ++PVINEND V T EI+ GDND L+AL A L AD L++LTD+ G++ ADPR Sbjct: 125 LRALVELKVIPVINENDTVVTDEIRFGDNDTLAALVANLVEADLLVILTDRDGMFDADPR 184 Query: 181 SNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPG 240 +N A+LI + D AL A+AG LG GGM TKL+AA +A R+G TII G Sbjct: 185 NNSDAQLIYEARADDPALDAVAGSVGGALGRGGMQTKLRAARLAARSGAHTIIVGGRIER 244 Query: 241 VIGDVMEGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKG 299 V+ + G +GTL + L RK+W+ G G + +D+GA +A+ + SLLP G Sbjct: 245 VLDRLKAGERIGTLLSPERGMLAARKQWLAGHLQTRGTLVLDDGAVSALSQGNKSLLPVG 304 Query: 300 IKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAV 359 +K V G+F RGE++ +GR+IA G++ Y++ ++I G S I +LGY P V Sbjct: 305 VKLVQGSFRRGEMVVCVAPDGREIARGLANYSALEAQKIIGQSSDAIVGLLGYMAEPELV 364 Query: 360 HRDDMI 365 HRD++I Sbjct: 365 HRDNLI 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: 363 Number of extensions: 11 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 GFF4601 PS417_23545 (gamma-glutamyl 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.20767.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-133 429.0 0.8 8.9e-133 428.8 0.8 1.0 1 lcl|FitnessBrowser__WCS417:GFF4601 PS417_23545 gamma-glutamyl kinas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF4601 PS417_23545 gamma-glutamyl kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 428.8 0.8 8.9e-133 8.9e-133 2 362 .. 10 370 .. 9 371 .. 0.99 Alignments for each domain: == domain 1 score: 428.8 bits; conditional E-value: 8.9e-133 TIGR01027 2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQ 76 r VvK+Gs++Lt++ + l+r+ ++ veq+ +l++aG e+v+vsSGavaaG+++Lg + rp ++e Qa+aa+GQ lcl|FitnessBrowser__WCS417:GFF4601 10 RWVVKIGSALLTADGKGLDRAAMSVWVEQMVALHEAGVELVLVSSGAVAAGMSRLGWTARPSAMHELQAAAAIGQ 84 78************************************************************************* PP TIGR01027 77 grLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsal 151 L++++e++f+ +g+++aQiLLt++dls+r+rylNar+tl++l+el+v+p++NENDtv ++ei+fGDNDtL+al lcl|FitnessBrowser__WCS417:GFF4601 85 MGLVQAWESSFADHGRHTAQILLTHDDLSDRKRYLNARSTLRALVELKVIPVINENDTVVTDEIRFGDNDTLAAL 159 *************************************************************************** PP TIGR01027 152 vaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragve 226 va+lveAdlLv+ltd dg++dadpr+n+dA+li e ++ + +l+avags g ++G GGm+tKl aa+lA+r+g + lcl|FitnessBrowser__WCS417:GFF4601 160 VANLVEADLLVILTDRDGMFDADPRNNSDAQLIYEARADDPALDAVAGSVGGALGRGGMQTKLRAARLAARSGAH 234 *************************************************************************** PP TIGR01027 227 viiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvveve 301 +ii+ g+ + + +l +++ +gtl+ +++ l +rkqw++ +++++G++++d+ga++al++ +ksLlp+gv v+ lcl|FitnessBrowser__WCS417:GFF4601 235 TIIVGGRIERVLDRLKAGERIGTLLSPERGMLAARKQWLAGHLQTRGTLVLDDGAVSALSQGNKSLLPVGVKLVQ 309 *******9999999************************************************************* PP TIGR01027 302 gnFsrgevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362 g+F+rge+v ++a++g+ei++gl+nys+ e +ki g++s+ i +Lgy + e vhrdnl+ lcl|FitnessBrowser__WCS417:GFF4601 310 GSFRRGEMVVCVAPDGREIARGLANYSALEAQKIIGQSSDAIVGLLGYMAEPELVHRDNLI 370 ***********************************************************97 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: 10.30 // [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