Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate Ac3H11_2067 Glucokinase (EC 2.7.1.2)
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 Glucokinase (EC 2.7.1.2) Length = 325 Score = 227 bits (579), Expect = 3e-64 Identities = 127/298 (42%), Positives = 177/298 (59%), Gaps = 4/298 (1%) Query: 6 LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEV-KDGCIAIA 64 L+ D+GGTN RLA +G ++ + +P+++A + YL+E V ++ IA Sbjct: 6 LLADIGGTNIRLAWQASPTGPLNDTRVLPCAQFPTVDAALAAYLQEVGVPTPREAAFGIA 65 Query: 65 CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124 P+TGD + MTNH+W+FS +++ GF L +INDFTA+++A+P+L E L GG Sbjct: 66 NPVTGDAIRMTNHSWSFSQRAVREAFGFERLVVINDFTALALALPLLTPEQLRPVGGGAA 125 Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLP--GEGGHVDFAPNSEEEAIILEILRAEIG 182 V G IA+ G GTGLGV+ LV + +P GEGGHV A ++ E +L IL+ G Sbjct: 126 VPGAAIALLGPGTGLGVSGLVFPPGSHLGVPLSGEGGHVTLAAQTQREFDVLAILQERYG 185 Query: 183 HVSAERVLSGPGLVNLYRAIVKADNRLPENL-KPKDITERALADSCTDCRRALSLFCVIM 241 HVSAER + G GLV+LY A+ + R + + +TE AL + AL LFC + Sbjct: 186 HVSAERAVCGAGLVDLYHALRRLAQRGGKEISSAAQVTELALQANDPLALEALELFCGFL 245 Query: 242 GRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLI 299 G GNLAL LG GGVFI GG+VPR +F S FRA FE KGRF+ Y+ IP ++I Sbjct: 246 GSVAGNLALTLGARGGVFIGGGMVPRLGAWFDQSPFRARFESKGRFQSYLAGIPCWVI 303 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: 18 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: 321 Length of database: 325 Length adjustment: 28 Effective length of query: 293 Effective length of database: 297 Effective search space: 87021 Effective search space used: 87021 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 Ac3H11_2067 (Glucokinase (EC 2.7.1.2))
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.2118.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-90 287.4 0.0 8e-90 287.3 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 Glucokinase (EC 2.7.1.2) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 Glucokinase (EC 2.7.1.2) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 287.3 0.0 8e-90 8e-90 1 314 [. 6 314 .. 6 315 .. 0.94 Alignments for each domain: == domain 1 score: 287.3 bits; conditional E-value: 8e-90 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaia 62 l++diGGtn rla + +g ++ +++ + +fp + a++ yl+e + p +++f ia lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 6 LLADIGGTNIRLAWQASPTGPLNDTRVLPCAQFPTVDAALAAYLQEVG--VPTPREAAFGIA 65 79************888899*************************975..56778******* PP TIGR00749 63 tPiigdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakvee 124 P++gd +r+tn++W++s +++ +++++l +indf+a a+a++ l e+l +gg +++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 66 NPVTGDAIRMTNHSWSFSQRAVREAFGFERLVVINDFTALALALPLLTPEQLRPVGGGAAVP 127 ************************************************************** PP TIGR00749 125 saaiailGaGtGlGvatliqqsdgry.kvlageGghvdfaPrseleillleylrkkygrvsa 185 +aaia+lG+GtGlGv+ l+ ++ + l+geGghv +a + + e+ +l +l+++yg+vsa lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 128 GAAIALLGPGTGLGVSGLVFPPGSHLgVPLSGEGGHVTLAAQTQREFDVLAILQERYGHVSA 189 ****************99975554442669******************************** PP TIGR00749 186 ervlsGsGlvliyealskrkgerevsklskeelkekdiseaalegsdvlarralelflsilG 247 er + G+Glv +y+al++ ++ ke +++e al+ +d+la +alelf++ lG lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 190 ERAVCGAGLVDLYHALRRLA-----QRGGKEISSAAQVTELALQANDPLALEALELFCGFLG 246 ****************9988.....667777778899************************* PP TIGR00749 248 alagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvl.kkk 308 ++agnlal+lgarGGv++ GG+vPr+ ++++s+fra+fe kGr++++la iP v+ ++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 247 SVAGNLALTLGARGGVFIGGGMVPRLGAWFDQSPFRARFESKGRFQSYLAGIPCWVIDpGAT 308 *******************************************************9952477 PP TIGR00749 309 vGllGa 314 + l Ga lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2067 309 PALHGA 314 888777 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (325 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: 6.86 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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