Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate HSERO_RS17870 HSERO_RS17870 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__HerbieS:HSERO_RS17870 Length = 333 Score = 245 bits (625), Expect = 1e-69 Identities = 133/313 (42%), Positives = 175/313 (55%), Gaps = 2/313 (0%) Query: 6 LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLE-EHKVEVKDGCIAIA 64 L+ D+GGTNAR AL + G I Q + G DY ++ YL+ V+ +AIA Sbjct: 18 LLADIGGTNARFAL-ETGPGRIEQVQILRGADYGEFTDAVQAYLKLAGHPPVRHAVVAIA 76 Query: 65 CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124 P+ GD + MTNH WAFSI ++ LGF L ++NDFTA+SMA+P L+ + L Q GG P Sbjct: 77 NPVQGDQIKMTNHDWAFSIEAARQLLGFELLLVVNDFTALSMAVPQLRADELQQVGGGAP 136 Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHV 184 G PI + GAGTGLGV L+H D W+ L EGGH FAP EA +L HV Sbjct: 137 KPGAPIGLVGAGTGLGVGGLLHADGHWLPLASEGGHAAFAPADPREAAVLAYAWQFHEHV 196 Query: 185 SAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRF 244 SAER++SGPGL ++RA++ D L I E A C+ L+LFC ++G Sbjct: 197 SAERLVSGPGLELIHRALLAIDGHPAAELSAAQIVEGARQHGDALCQETLALFCSMLGTV 256 Query: 245 GGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNP 304 +LAL LG GG++I G+VP ++F S FRA FE+KGR IP Y+I + P Sbjct: 257 AADLALTLGALGGIYIGVGVVPHLGDYFARSPFRARFENKGRMSVLTKAIPTYVITAEYP 316 Query: 305 GLLGSGAHLRQTL 317 G A L L Sbjct: 317 AFTGVSAILADRL 329 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: 358 Number of extensions: 15 Number of successful extensions: 3 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: 333 Length adjustment: 28 Effective length of query: 293 Effective length of database: 305 Effective search space: 89365 Effective search space used: 89365 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 HSERO_RS17870 HSERO_RS17870 (glucokinase)
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.13614.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-97 310.2 0.0 9.8e-97 309.9 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS17870 HSERO_RS17870 glucokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS17870 HSERO_RS17870 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 309.9 0.0 9.8e-97 9.8e-97 1 313 [. 18 320 .. 18 322 .. 0.96 Alignments for each domain: == domain 1 score: 309.9 bits; conditional E-value: 9.8e-97 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpi.kgcfaiatPiig 67 l++diGGtnar+al e pg+ieqv+++++ d+ +++++v+ yl+ a p+ ++ +aia P+ g lcl|FitnessBrowser__HerbieS:HSERO_RS17870 18 LLADIGGTNARFAL-ETGPGRIEQVQILRGADYGEFTDAVQAYLKLAGH---PPVrHAVVAIANPVQG 81 79************.****************************987654...466579********** PP TIGR00749 68 dfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGt 135 d +++tn+dWa+sie +q l+++ l ++ndf+a ++a++ l+ ++l q+gg ++++a+i ++GaGt lcl|FitnessBrowser__HerbieS:HSERO_RS17870 82 DQIKMTNHDWAFSIEAARQLLGFELLLVVNDFTALSMAVPQLRADELQQVGGGAPKPGAPIGLVGAGT 149 ******************************************************************** PP TIGR00749 136 GlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealsk 203 GlGv l++ +dg++ la+eGgh+ faP ++ e+ +l y+ + ++vsaer++sG+Gl li++al lcl|FitnessBrowser__HerbieS:HSERO_RS17870 150 GLGVGGLLH-ADGHWLPLASEGGHAAFAPADPREAAVLAYAWQFHEHVSAERLVSGPGLELIHRALLA 216 *********.*********************************************************9 PP TIGR00749 204 rkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivP 271 +g+ + +el +i e a + d+l++++l lf+s+lG++a++lal+lga GG+y+ G+vP lcl|FitnessBrowser__HerbieS:HSERO_RS17870 217 IDGH------PAAELSAAQIVEGARQHGDALCQETLALFCSMLGTVAADLALTLGALGGIYIGVGVVP 278 9953......45666788899*********************************************** PP TIGR00749 272 rfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllG 313 ++ +++ +s+fra+fe+kGr+ l + iP +v+ + + + G lcl|FitnessBrowser__HerbieS:HSERO_RS17870 279 HLGDYFARSPFRARFENKGRMSVLTKAIPTYVITAEYPAFTG 320 *********************************999988777 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (333 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: 10.06 // [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