Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate 16493 b2388 glucokinase (NCBI)
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__Keio:16493 Length = 321 Score = 648 bits (1672), Expect = 0.0 Identities = 321/321 (100%), Positives = 321/321 (100%) Query: 1 MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGC 60 MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGC Sbjct: 1 MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGC 60 Query: 61 IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFG 120 IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFG Sbjct: 61 IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFG 120 Query: 121 GAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAE 180 GAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAE Sbjct: 121 GAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAE 180 Query: 181 IGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI 240 IGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI Sbjct: 181 IGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI 240 Query: 241 MGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIV 300 MGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIV Sbjct: 241 MGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIV 300 Query: 301 HDNPGLLGSGAHLRQTLGHIL 321 HDNPGLLGSGAHLRQTLGHIL Sbjct: 301 HDNPGLLGSGAHLRQTLGHIL 321 Lambda K H 0.322 0.141 0.426 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: 533 Number of extensions: 9 Number of successful extensions: 1 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: 321 Length of database: 321 Length adjustment: 28 Effective length of query: 293 Effective length of database: 293 Effective search space: 85849 Effective search space used: 85849 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 bits)
Align candidate 16493 b2388 (glucokinase (NCBI))
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))
# 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.carbon/TIGR00749.hmm # target sequence database: /tmp/gapView.14499.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00749 [M=315] Accession: TIGR00749 Description: glk: glucokinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-160 519.4 0.0 1.9e-160 519.2 0.0 1.0 1 lcl|FitnessBrowser__Keio:16493 b2388 glucokinase (NCBI) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:16493 b2388 glucokinase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 519.2 0.0 1.9e-160 1.9e-160 1 315 [] 6 310 .. 6 310 .. 1.00 Alignments for each domain: == domain 1 score: 519.2 bits; conditional E-value: 1.9e-160 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrltnldWal 79 lvgd+GGtnarlal+++a+gei+q+ktys++d+psleav+rvylee+kve+kd gc+aia+Pi+gd+v++tn++Wa+ lcl|FitnessBrowser__Keio:16493 6 LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKD---GCIAIACPITGDWVAMTNHTWAF 81 89***************************************************...*********************** PP TIGR00749 80 sieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqsdgrykvlageGg 158 si+e+k++l++++le+indf+av++ai++lk+e+liq+gga+++e+++ia++GaGtGlGva+l++ +d+r+++l+geGg lcl|FitnessBrowser__Keio:16493 82 SIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEPVEGKPIAVYGAGTGLGVAHLVH-VDKRWVSLPGEGG 159 *****************************************************************.************* PP TIGR00749 159 hvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelkekdiseaalegsdvlarr 237 hvdfaP+se+e+++le+lr+++g+vsaervlsG+Glv++y+a++k++ ++l+ e+lk+kdi+e+al++s++++rr lcl|FitnessBrowser__Keio:16493 160 HVDFAPNSEEEAIILEILRAEIGHVSAERVLSGPGLVNLYRAIVKAD-----NRLP-ENLKPKDITERALADSCTDCRR 232 ***********************************************.....****.9********************* PP TIGR00749 238 alelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 al+lf++i+G+++gnlal+lg++GGv++aGGivPrf+e++k+s+fraafedkGr+ke++++iPv++++++++GllG+g lcl|FitnessBrowser__Keio:16493 233 ALSLFCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNPGLLGSG 310 ****************************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (321 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: 8.76 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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