Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate Pf6N2E2_5103 Glutamate 5-kinase (EC 2.7.2.11) / RNA-binding C-terminal domain PUA
Query= BRENDA::P0A7B5 (367 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5103 Length = 372 Score = 298 bits (764), Expect = 1e-85 Identities = 160/366 (43%), Positives = 229/366 (62%), Gaps = 1/366 (0%) Query: 1 MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60 ++ +Q VVK+G+++LT + L+R + V Q LH AG +V+V+SGA+AAG L Sbjct: 5 VTGAQRWVVKIGSALLTADGKGLDRQAMAVWVEQMVALHEAGVELVLVSSGAVAAGMSRL 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 GWTSRPSAMHELQAAAAIGQMGLVQAWESSFAEHGRHTAQILLTHDDLSDRKRYLNARST 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 +NP A+LI + D AL A+AG + LG GGM TKL+AA +A R+G TII G Sbjct: 185 NNPDAKLIYEARADDPALDAVAGGTGGALGRGGMQTKLRAARLAARSGAHTIIVGGRLER 244 Query: 241 VIGDVMEGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKG 299 V+ + G +GTL + L RK+W+ G G + +D GA A+ + SLLP G Sbjct: 245 VLDRLKAGERIGTLLSPERGMLAARKQWLAGHLQTRGTLVLDAGAVVALSQGNKSLLPVG 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: 368 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: 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 Pf6N2E2_5103 (Glutamate 5-kinase (EC 2.7.2.11) / RNA-binding C-terminal domain PUA)
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.3570.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-134 434.0 0.5 2.8e-134 433.8 0.5 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5103 Glutamate 5-kinase (EC 2.7.2.11) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5103 Glutamate 5-kinase (EC 2.7.2.11) / RNA-binding C-terminal domain PUA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 433.8 0.5 2.8e-134 2.8e-134 2 362 .. 10 370 .. 9 371 .. 0.99 Alignments for each domain: == domain 1 score: 433.8 bits; conditional E-value: 2.8e-134 TIGR01027 2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkkl 65 r VvK+Gs++Lt++ + l+r+ +a veq+ +l++aG e+v+vsSGavaaG+++Lg ++rp + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5103 10 RWVVKIGSALLTADGKGLDRQAMAVWVEQMVALHEAGVELVLVSSGAVAAGMSRLGWTSRPSAM 73 78************************************************************** PP TIGR01027 66 aekQalaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpiv 129 +e Qa+aa+GQ L++++e++f+++g+++aQiLLt++dls+r+rylNar+tl++l+el+v+p++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5103 74 HELQAAAAIGQMGLVQAWESSFAEHGRHTAQILLTHDDLSDRKRYLNARSTLRALVELKVIPVI 137 **************************************************************** PP TIGR01027 130 NENDtvaveeikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieee 193 NENDtv ++ei+fGDNDtL+alva+lveAdlLv+ltd dg++dadpr+npdAkli e ++ + + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5103 138 NENDTVVTDEIRFGDNDTLAALVANLVEADLLVILTDRDGMFDADPRNNPDAKLIYEARADDPA 201 **************************************************************** PP TIGR01027 194 lkavagssgssvGTGGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkk 257 l+avag++g ++G GGm+tKl aa+lA+r+g ++ii+ g+ + + +l +++ +gtl+ +++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5103 202 LDAVAGGTGGALGRGGMQTKLRAARLAARSGAHTIIVGGRLERVLDRLKAGERIGTLLSPERGM 265 *****************************************999******************** PP TIGR01027 258 lknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeig 321 l +rkqw++ +++++G++++d+ga+ al++ +ksLlp+gv v+g+F+rge+v ++a++g+ei+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5103 266 LAARKQWLAGHLQTRGTLVLDAGAVVALSQGNKSLLPVGVKLVQGSFRRGEMVVCVAPDGREIA 329 **************************************************************** PP TIGR01027 322 kglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362 +gl+nys+ e +ki g++s+ i +Lgy + e vhrdnl+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5103 330 RGLANYSALEAQKIIGQSSDAIVGLLGYMAEPELVHRDNLI 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.45 // [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