Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_015819474.1 TERTU_RS12940 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >NCBI__GCF_000023025.1:WP_015819474.1 Length = 319 Score = 242 bits (617), Expect = 1e-68 Identities = 133/316 (42%), Positives = 186/316 (58%), Gaps = 6/316 (1%) Query: 5 ALVGDVGGTNARLALCD-IASGE--ISQAKTYSGLDYPSLEAVIRVYLEE-HKVEVKDGC 60 ++V D+GGTNAR AL +G+ I + +G +Y +R Y++ ++ C Sbjct: 4 SIVADIGGTNARFALVTGTENGQFVIENIQILNGAEYEGFADALRAYMDSLGSLKPFSAC 63 Query: 61 IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQF- 119 +AIA PI GD V MTN +W+F+ + ++K GF +INDF A+++A L L+ Sbjct: 64 VAIAGPIAGDSVQMTNLSWSFTQSGIRKAFGFEKFAVINDFGALAVATSALNPTDLVSVK 123 Query: 120 GGAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRA 179 GG+ EG A+ G GTGLGVA L + W+ +P EGGHV+ AP S E +++ A Sbjct: 124 GGSRNPEGNK-AIMGPGTGLGVAGLAYTGSNWLPIPSEGGHVNIAPASALECEVIKAAIA 182 Query: 180 EIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCV 239 GHVSAE +SGPGLVNLYRA+ + + P L+PKDIT A++ + C L+LFC Sbjct: 183 THGHVSAETFISGPGLVNLYRALCEVNGVSPRELQPKDITADAMSAADQTCVYTLNLFCS 242 Query: 240 IMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLI 299 +G GNLAL G GGV++AGGI+PR L+F K S F++ F +KG YV DIPV +I Sbjct: 243 FLGTVAGNLALTYGASGGVYLAGGILPRMLDFLKDSDFKSRFSNKGVMSHYVDDIPVDII 302 Query: 300 VHDNPGLLGSGAHLRQ 315 H LG+ L Q Sbjct: 303 AHPQTAFLGAATWLAQ 318 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: 325 Number of extensions: 14 Number of successful extensions: 2 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: 319 Length adjustment: 28 Effective length of query: 293 Effective length of database: 291 Effective search space: 85263 Effective search space used: 85263 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 WP_015819474.1 TERTU_RS12940 (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.21337.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-94 302.5 0.2 2.1e-94 302.3 0.2 1.0 1 lcl|NCBI__GCF_000023025.1:WP_015819474.1 TERTU_RS12940 glucokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023025.1:WP_015819474.1 TERTU_RS12940 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 302.3 0.2 2.1e-94 2.1e-94 2 315 .] 6 313 .. 5 313 .. 0.96 Alignments for each domain: == domain 1 score: 302.3 bits; conditional E-value: 2.1e-94 TIGR00749 2 vgdiGGtnarlalv...evapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiig 67 v+diGGtnar+alv e ie+++++++ +++ + +++r y++ +lk p +c+aia+Pi g lcl|NCBI__GCF_000023025.1:WP_015819474.1 6 VADIGGTNARFALVtgtENGQFVIENIQILNGAEYEGFADALRAYMDSLG-SLK-PFSACVAIAGPIAG 72 89************988888888**********************98754.555.8************* PP TIGR00749 68 dfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtG 136 d v++tnl+W+++ +++ ++++k +indf a a+a +al+ dl+ ++g ++++ +ai+G+GtG lcl|NCBI__GCF_000023025.1:WP_015819474.1 73 DSVQMTNLSWSFTQSGIRKAFGFEKFAVINDFGALAVATSALNPTDLVSVKGGSRNPEGNKAIMGPGTG 141 ********************************************************************* PP TIGR00749 137 lGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrk 205 lGva l + ++ +++eGghv+ aP s le+ +++ + + g+vsae ++sG+Glv++y+al + + lcl|NCBI__GCF_000023025.1:WP_015819474.1 142 LGVAGLAY-TGSNWLPIPSEGGHVNIAPASALECEVIKAAIATHGHVSAETFISGPGLVNLYRALCEVN 209 ******99.7789***************************************************98655 PP TIGR00749 206 gerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfi 274 +s el++kdi+ a+ d + +l+lf+s lG++agnlal+ ga GGvy+aGGi+Pr++ lcl|NCBI__GCF_000023025.1:WP_015819474.1 210 ------GVSPRELQPKDITADAMSAADQTCVYTLNLFCSFLGTVAGNLALTYGASGGVYLAGGILPRML 272 ......678899********************************************************* PP TIGR00749 275 ellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 ++lk s f+++f++kG + +++ +iPv ++ + ++ +lGa+ lcl|NCBI__GCF_000023025.1:WP_015819474.1 273 DFLKDSDFKSRFSNKGVMSHYVDDIPVDIIAHPQTAFLGAA 313 ***********************************999996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (319 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: 8.41 // [ok]
This GapMind analysis is from Sep 24 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