Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate 206361 DVU0930 glutamate 5-kinase
Query= BRENDA::P0A7B5 (367 letters) >MicrobesOnline__882:206361 Length = 380 Score = 265 bits (678), Expect = 1e-75 Identities = 156/369 (42%), Positives = 230/369 (62%), Gaps = 8/369 (2%) Query: 1 MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60 + +++ +VVK+G++VLT + +N A I L Q + L +G R+V+V+SGA+AAGR L Sbjct: 11 LREARCVVVKVGSAVLTTETG-VNLAVIDSLAAQLSALQESGKRVVLVSSGAVAAGRSAL 69 Query: 61 GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120 A + KQ +AVGQSRL+ +++ F+ YG Q+LLTR D+ +RERFLNAR+T Sbjct: 70 RDCCEIAGMPHKQAASAVGQSRLMHHYDEAFARYGHLSAQVLLTRDDLRNRERFLNARNT 129 Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180 +ALLD ++PV+NEND VA E+K GDND L++L + D + LT G+Y +P+ Sbjct: 130 FQALLDWGVIPVVNENDTVAVQELKFGDNDCLASLLLNVVEGDLYVNLTSASGVYADNPQ 189 Query: 181 SNPQAEL---IKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGS 237 +NP+A + I+DV+ +D L + G S +GTGGM +KL AA A + G+ T+I G Sbjct: 190 TNPEAGILPCIEDVHTLD--LDVMCGGKTS-VGTGGMYSKLLAASRAAQLGVPTLILPGR 246 Query: 238 KPGVIGDVMEGISVGTLFHAQATPLENRKRWI-FGAPPAGEITVDEGATAAILERGSSLL 296 +P ++ G VGT +A + RK W+ + + P+G +TVDEGA A+L++G SLL Sbjct: 247 EPRILERAFSGEPVGTWVRPEARVVSRRKYWLAYQSEPSGTVTVDEGAARALLQQGGSLL 306 Query: 297 PKGIKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGP 356 P G+ V+G F G ++RI +G IA G+S Y L RI GH E+ AILG + P Sbjct: 307 PGGVCDVSGAFEPGALVRIAGPDGTVIAVGLSNYGDRDLVRIKGHRRHEVAAILGDAHFP 366 Query: 357 VAVHRDDMI 365 VHRD+M+ Sbjct: 367 EVVHRDNML 375 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: 375 Number of extensions: 23 Number of successful extensions: 4 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: 380 Length adjustment: 30 Effective length of query: 337 Effective length of database: 350 Effective search space: 117950 Effective search space used: 117950 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 206361 DVU0930 (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.10806.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-123 399.0 0.0 1.2e-123 398.8 0.0 1.0 1 lcl|MicrobesOnline__882:206361 DVU0930 glutamate 5-kinase Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:206361 DVU0930 glutamate 5-kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 398.8 0.0 1.2e-123 1.2e-123 3 362 .. 17 375 .. 15 376 .. 0.99 Alignments for each domain: == domain 1 score: 398.8 bits; conditional E-value: 1.2e-123 TIGR01027 3 iVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQgrLmk 81 +VvK+Gs++Lt+e+g ++++ + +l++q+++l++ G++vv+vsSGavaaG +aL + + +kQa++aVGQ+rLm+ lcl|MicrobesOnline__882:206361 17 VVVKVGSAVLTTETG-VNLAVIDSLAAQLSALQESGKRVVLVSSGAVAAGRSALRDCCEIAGMPHKQAASAVGQSRLMH 94 9***********999.*************************************************************** PP TIGR01027 82 lyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaalveAdl 160 +y+++f++yg +aQ+LLtr+dl++rer+lNarnt+++ll++gv+p+vNENDtvav+e+kfGDND L+ l+ ++ve dl lcl|MicrobesOnline__882:206361 95 HYDEAFARYGHLSAQVLLTRDDLRNRERFLNARNTFQALLDWGVIPVVNENDTVAVQELKFGDNDCLASLLLNVVEGDL 173 ******************************************************************************* PP TIGR01027 161 LvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviiasgekpekia 239 v lt++ g+y ++p+tnp+A +++ +e++++ v ++ +svGTGGm +Kl aa+ A+++gv+++i++g++p + lcl|MicrobesOnline__882:206361 174 YVNLTSASGVYADNPQTNPEAGILPCIEDVHTLDLDVMCGGKTSVGTGGMYSKLLAASRAAQLGVPTLILPGREPRILE 252 ********************************999999999999*********************************** PP TIGR01027 240 dlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrgevveilaeegq 318 ++ ++++vgt + ++++ ++ rk w++++se++G+++vdega++all++g sLlp gv +v+g F+ g v+i ++g+ lcl|MicrobesOnline__882:206361 253 RAFSGEPVGTWVRPEARVVSRRKYWLAYQSEPSGTVTVDEGAARALLQQGGSLLPGGVCDVSGAFEPGALVRIAGPDGT 331 ******************************************************************************* PP TIGR01027 319 eigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362 i+ gl+ny +l +ikg++ +e++++Lg + evvhrdn++ lcl|MicrobesOnline__882:206361 332 VIAVGLSNYGDRDLVRIKGHRRHEVAAILGDAHFPEVVHRDNML 375 ******************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (380 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.09 // [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