Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate 8500629 DvMF_1377 gamma-glutamyl kinase (RefSeq)
Query= BRENDA::P0A7B5 (367 letters) >FitnessBrowser__Miya:8500629 Length = 395 Score = 261 bits (668), Expect = 2e-74 Identities = 150/369 (40%), Positives = 226/369 (61%), Gaps = 8/369 (2%) Query: 1 MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60 ++D++ +VVK+G++VLT G L+ A + L Q + + G R+V+V+SGA+AAGR L Sbjct: 26 LADARCVVVKVGSAVLTNGEG-LDLAMVESLAGQLSAVQEGGRRVVLVSSGAVAAGRGVL 84 Query: 61 GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120 A + +Q +A+GQSRL+ +++ F+ G Q+LLTR D++ R RFLNAR+T Sbjct: 85 RSCCEIAGMPHRQAASAIGQSRLMHHYDEAFARCGRISAQVLLTRDDLKSRNRFLNARNT 144 Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180 ALLD +PV+NEND VA ++K GDND L++L + AD + +T G++ +P+ Sbjct: 145 FAALLDWGAIPVVNENDTVAVHDLKFGDNDCLASLLLNIVEADLFVNMTSAGGVFAENPQ 204 Query: 181 SNPQA---ELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGS 237 NP A I DV+G+D L + G S +GTGGM +KL +A A + G+ T+I G Sbjct: 205 DNPDACVMACIDDVHGLD--LNGLCGGKTS-VGTGGMYSKLLSARRAAQIGVPTLIVPGR 261 Query: 238 KPGVIGDVMEGISVGTLFHAQATPLENRKRWI-FGAPPAGEITVDEGATAAILERGSSLL 296 +P V+ V G ++GT A A + RK W+ + + PAG +TVDEGA A+L+ G SLL Sbjct: 262 EPDVLARVFAGEAIGTWVRADARTVSRRKYWLAYQSDPAGTVTVDEGAARALLQGGKSLL 321 Query: 297 PKGIKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGP 356 P G+ +V G F G ++R+ +G I G+S Y + LRRI GH E+ AILG + P Sbjct: 322 PGGVCAVEGGFGSGALVRVAAQDGTVIGVGLSNYAAAELRRIMGHKRHEVAAILGDAHYP 381 Query: 357 VAVHRDDMI 365 +HRD+++ Sbjct: 382 EVIHRDNLL 390 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: 382 Number of extensions: 20 Number of successful extensions: 5 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: 395 Length adjustment: 30 Effective length of query: 337 Effective length of database: 365 Effective search space: 123005 Effective search space used: 123005 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: 50 (23.9 bits)
Align candidate 8500629 DvMF_1377 (gamma-glutamyl kinase (RefSeq))
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.23077.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-119 382.9 0.0 9.7e-119 382.7 0.0 1.0 1 lcl|FitnessBrowser__Miya:8500629 DvMF_1377 gamma-glutamyl kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8500629 DvMF_1377 gamma-glutamyl kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 382.7 0.0 9.7e-119 9.7e-119 3 362 .. 32 390 .. 30 391 .. 0.99 Alignments for each domain: == domain 1 score: 382.7 bits; conditional E-value: 9.7e-119 TIGR01027 3 iVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQgrL 79 +VvK+Gs++Lt+++g l+++++++l+ q++++++ G++vv+vsSGavaaG L + + ++Qa++a+GQ+rL lcl|FitnessBrowser__Miya:8500629 32 VVVKVGSAVLTNGEG-LDLAMVESLAGQLSAVQEGGRRVVLVSSGAVAAGRGVLRSCCEIAGMPHRQAASAIGQSRL 107 9*************9.************************************************************* PP TIGR01027 80 mklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaalv 156 m++y+++f++ g+ +aQ+LLtr+dl++r+r+lNarnt+ +ll++g++p+vNENDtvav+++kfGDND L+ l+ ++v lcl|FitnessBrowser__Miya:8500629 108 MHHYDEAFARCGRISAQVLLTRDDLKSRNRFLNARNTFAALLDWGAIPVVNENDTVAVHDLKFGDNDCLASLLLNIV 184 ***************************************************************************** PP TIGR01027 157 eAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviiasge 233 eAdl v +t++ g++ ++p+ npdA ++ +++++ + ++ +svGTGGm +Kl +a+ A++ gv+++i++g+ lcl|FitnessBrowser__Miya:8500629 185 EADLFVNMTSAGGVFAENPQDNPDACVMACIDDVHGLDLNGLCGGKTSVGTGGMYSKLLSARRAAQIGVPTLIVPGR 261 **********************************99888877777899***************************** PP TIGR01027 234 kpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrgevv 310 +p+ +a++ +++a+gt + a +++++ rk w++++s+++G+++vdega++all+ gksLlp gv +veg F +g v lcl|FitnessBrowser__Miya:8500629 262 EPDVLARVFAGEAIGTWVRADARTVSRRKYWLAYQSDPAGTVTVDEGAARALLQGGKSLLPGGVCAVEGGFGSGALV 338 ***************************************************************************** PP TIGR01027 311 eilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362 ++ a++g+ ig gl+ny ++el++i+g+k +e++++Lg + ev+hrdnl+ lcl|FitnessBrowser__Miya:8500629 339 RVAAQDGTVIGVGLSNYAAAELRRIMGHKRHEVAAILGDAHYPEVIHRDNLL 390 **************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (395 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 12.73 // [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