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) >FitnessBrowser__acidovorax_3H11:Ac3H11_2067 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.20876.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: 6.74 // [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