Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate GFF2219 HP15_2173 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__Marino:GFF2219 Length = 321 Score = 254 bits (649), Expect = 2e-72 Identities = 136/313 (43%), Positives = 185/313 (59%), Gaps = 1/313 (0%) Query: 2 TKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDG-C 60 T Y+LVGD+GGTNAR AL + + + K +Y +L+ +R YL V DG C Sbjct: 4 THYSLVGDIGGTNARFALVEQGTVQPRAIKILPCGEYANLDDAVRDYLARVGVSEVDGAC 63 Query: 61 IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFG 120 +A+A P+ G V MTN+ W F E++ G+S ++INDFTA+++ +P + +HL+ Sbjct: 64 LAVASPVRGTQVRMTNNHWLFDTEEVRAQFGWSRFKVINDFTAMALGVPHVANDHLVHVC 123 Query: 121 GAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAE 180 G +P V G GTGLGV+ LV ++ WV L EGGHVDFAP + E +L IL+A Sbjct: 124 GGPGDSRRPRLVMGPGTGLGVSGLVPIEHGWVPLMTEGGHVDFAPTDDAEMAVLRILKAR 183 Query: 181 IGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI 240 G VS ER+L G GL+NLY+A + P+ IT A+ ++ R LS FC I Sbjct: 184 FGRVSVERILCGQGLLNLYQAHAEIQGVAAPLDAPEKITAAAVENTDRLARHTLSHFCEI 243 Query: 241 MGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIV 300 +GR GN L LG+ GGVF+ GGI+PRFLEFF S FR FEDKGR + + PVY++ Sbjct: 244 LGRVAGNGVLTLGSTGGVFLCGGILPRFLEFFLESPFRNGFEDKGRMRPLLEFTPVYVVT 303 Query: 301 HDNPGLLGSGAHL 313 GLLG+ L Sbjct: 304 EPYTGLLGAAEAL 316 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: 320 Number of extensions: 13 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: 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 GFF2219 HP15_2173 (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.32064.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-98 315.7 0.0 2.1e-98 315.5 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF2219 HP15_2173 glucokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF2219 HP15_2173 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 315.5 0.0 2.1e-98 2.1e-98 1 315 [] 8 313 .. 8 313 .. 0.96 Alignments for each domain: == domain 1 score: 315.5 bits; conditional E-value: 2.1e-98 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrltnl 75 lvgdiGGtnar+alve + + +++k++ + ++ +l ++vr yl + v+ d +c+a+a+P+ g vr+tn+ lcl|FitnessBrowser__Marino:GFF2219 8 LVGDIGGTNARFALVEQGTVQPRAIKILPCGEYANLDDAVRDYLARVGVSEVD--GACLAVASPVRGTQVRMTNN 80 89******************************************998887666..7******************* PP TIGR00749 76 dWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqsdgry 150 +W + ee++ +++ ++ ++indf+a+a++++ + +++l+ + g + + + ++G+GtGlGv+ l++ + + lcl|FitnessBrowser__Marino:GFF2219 81 HWLFDTEEVRAQFGWSRFKVINDFTAMALGVPHVANDHLVHVCGGPGDSRRPRLVMGPGTGLGVSGLVP-IEHGW 154 *********************************************************************.9999* PP TIGR00749 151 kvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelkekdise 225 + l +eGghvdfaP+++ e+ +l++l++++grvs+er+l G+Gl ++y+a + +g + +++i+ lcl|FitnessBrowser__Marino:GFF2219 155 VPLMTEGGHVDFAPTDDAEMAVLRILKARFGRVSVERILCGQGLLNLYQAHAEIQG------VAAPLDAPEKITA 223 ************************************************99666553......3334458999*** PP TIGR00749 226 aalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiP 300 aa+e++d lar++l+ f+ ilG++agn l+lg+ GGv+++GGi+Prf+e++ +s+fr++fedkGr++ ll+ P lcl|FitnessBrowser__Marino:GFF2219 224 AAVENTDRLARHTLSHFCEILGRVAGNGVLTLGSTGGVFLCGGILPRFLEFFLESPFRNGFEDKGRMRPLLEFTP 298 *************************************************************************** PP TIGR00749 301 vqvvlkkkvGllGag 315 v+vv + +GllGa+ lcl|FitnessBrowser__Marino:GFF2219 299 VYVVTEPYTGLLGAA 313 *************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: 00:00:00.00 # Mc/sec: 10.17 // [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