Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate 6938397 Sama_2516 gamma-glutamyl kinase (RefSeq)
Query= BRENDA::P0A7B5 (367 letters) >FitnessBrowser__SB2B:6938397 Length = 379 Score = 441 bits (1133), Expect = e-128 Identities = 229/360 (63%), Positives = 277/360 (76%), Gaps = 1/360 (0%) Query: 7 LVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELP 66 +VVKLGTSVLT GS+ L++AH+VEL RQ A L +G +V+VTSGAIAAGREHLGYP LP Sbjct: 11 VVVKLGTSVLTSGSKSLDKAHMVELARQMAGLMKSGVEVVLVTSGAIAAGREHLGYPVLP 70 Query: 67 ATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLD 126 T+A+KQLLAAVGQS+LI W QLFSIYG+HVGQ+LLTRAD+ DRER+LNARDTL ALL Sbjct: 71 DTMANKQLLAAVGQSQLILAWSQLFSIYGLHVGQLLLTRADLHDRERYLNARDTLNALLA 130 Query: 127 NNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNPQAE 186 IVP+INENDAVAT EIKVGDNDNLSA AA+L AD L+LLTDQKGL+ ADPR P A Sbjct: 131 QGIVPIINENDAVATTEIKVGDNDNLSARAALLCDADLLMLLTDQKGLFDADPRKEPNAR 190 Query: 187 LIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVM 246 LI +V IDD+LR +AG SVSGLGTGGM+TKLQAAD+A RAG++ IIA+G P VI + Sbjct: 191 LIPEVEHIDDSLRLLAGGSVSGLGTGGMATKLQAADIARRAGVEVIIASGHHPEVIKKAV 250 Query: 247 EGISVGTLFHAQATPLENRKRWIFGAPPA-GEITVDEGATAAILERGSSLLPKGIKSVTG 305 +VGT F A +PLE+RK+WI P A G + +D GA AA+ RG SLL KGI V G Sbjct: 251 HREAVGTRFLAIESPLESRKQWILAGPKAKGRLLLDIGAVAAVTCRGRSLLSKGITGVEG 310 Query: 306 NFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMI 365 F RG+ + + + +GR +A G++RY S AL IAG HS EI+ +LGY+YG VHR+DM+ Sbjct: 311 QFERGDTLELVSPDGRVVARGMARYQSQALNLIAGKHSDEIEPLLGYDYGDAVVHRNDMV 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: 428 Number of extensions: 17 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: 379 Length adjustment: 30 Effective length of query: 337 Effective length of database: 349 Effective search space: 117613 Effective search space used: 117613 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 6938397 Sama_2516 (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.28652.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-150 486.2 0.2 3.8e-150 486.0 0.2 1.0 1 lcl|FitnessBrowser__SB2B:6938397 Sama_2516 gamma-glutamyl kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938397 Sama_2516 gamma-glutamyl kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 486.0 0.2 3.8e-150 3.8e-150 1 363 [] 9 371 .. 9 371 .. 1.00 Alignments for each domain: == domain 1 score: 486.0 bits; conditional E-value: 3.8e-150 TIGR01027 1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQg 77 +r+VvKlG+s+Lt++s++l++++++el++q+a l+k G evv+v+SGa+aaG e+Lg+p p ++a+kQ+laaVGQ+ lcl|FitnessBrowser__SB2B:6938397 9 RRVVVKLGTSVLTSGSKSLDKAHMVELARQMAGLMKSGVEVVLVTSGAIAAGREHLGYPVLPDTMANKQLLAAVGQS 85 59*************************************************************************** PP TIGR01027 78 rLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaa 154 +L+ ++++lfs+ygl+v+Q+LLtradl++rerylNar+tl++ll+ g+vpi+NEND+va++eik+GDND+Lsa a lcl|FitnessBrowser__SB2B:6938397 86 QLILAWSQLFSIYGLHVGQLLLTRADLHDRERYLNARDTLNALLAQGIVPIINENDAVATTEIKVGDNDNLSARAAL 162 ***************************************************************************** PP TIGR01027 155 lveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviias 231 l +AdlL+lltd++gL+dadpr++p+A+li+eve+i+++l+ +ag+s s +GTGGm+tKl+aa++A ragveviias lcl|FitnessBrowser__SB2B:6938397 163 LCDADLLMLLTDQKGLFDADPRKEPNARLIPEVEHIDDSLRLLAGGSVSGLGTGGMATKLQAADIARRAGVEVIIAS 239 ***************************************************************************** PP TIGR01027 232 gekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrge 308 g++pe i ++++ +avgt f a ++ l++rkqwila+++akG++++d ga++a++ +g+sLl +g+++veg+F+rg+ lcl|FitnessBrowser__SB2B:6938397 240 GHHPEVIKKAVHREAVGTRFLAIESPLESRKQWILAGPKAKGRLLLDIGAVAAVTCRGRSLLSKGITGVEGQFERGD 316 ***************************************************************************** PP TIGR01027 309 vveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlvl 363 ++e+++++g+ +++g+++y+s++l+ i+g++s+eie +Lgy + + vvhr+++v+ lcl|FitnessBrowser__SB2B:6938397 317 TLELVSPDGRVVARGMARYQSQALNLIAGKHSDEIEPLLGYDYGDAVVHRNDMVV 371 ****************************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (363 nodes) Target sequences: 1 (379 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: 7.19 // [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