Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_087504727.1 CBE68_RS03760 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >NCBI__GCF_002165625.1:WP_087504727.1 Length = 320 Score = 305 bits (782), Expect = 7e-88 Identities = 153/310 (49%), Positives = 199/310 (64%) Query: 6 LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIAIAC 65 L+ DVGGTN RLAL D E ++ + Y YP++ VIR YLEE V+ CIAIAC Sbjct: 7 LIADVGGTNIRLALVDEQGVEYTELRKYLCAQYPTITDVIRHYLEEVNASVRHACIAIAC 66 Query: 66 PITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEPV 125 P DW+ MTN++WAFS E+++ LG L IIND+TA+SM++P LK + ++Q G Sbjct: 67 PTNSDWIDMTNNSWAFSRREVQEELGLDALYIINDYTAISMSLPFLKDDQMVQVGPGMIE 126 Query: 126 EGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHVS 185 P AV G GTGLGVAHLV V+ W SLPGEGGHVDFAP + + I + L HVS Sbjct: 127 PAAPKAVLGPGTGLGVAHLVSVEGHWHSLPGEGGHVDFAPIDDVDNYIWKYLNKRYPHVS 186 Query: 186 AERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRFG 245 E++LSG GL+ +Y A+ + P DIT +A C C+ A+ FC ++G Sbjct: 187 YEQLLSGLGLIQIYEALCEMRGVTVIERTPADITTLGVAGECELCQAAVEQFCKVLGSHA 246 Query: 246 GNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNPG 305 GNLA+NLG FGGV++AGGIVPRF +F + S FRA FE KGRF +YV +P +LI + PG Sbjct: 247 GNLAMNLGAFGGVYVAGGIVPRFTDFVERSEFRARFEAKGRFTDYVRRVPTFLITEEQPG 306 Query: 306 LLGSGAHLRQ 315 LLG+ A+L Q Sbjct: 307 LLGAAAYLMQ 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: 325 Number of extensions: 13 Number of successful extensions: 1 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: 320 Length adjustment: 28 Effective length of query: 293 Effective length of database: 292 Effective search space: 85556 Effective search space used: 85556 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_087504727.1 CBE68_RS03760 (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.3216528.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-108 349.2 0.0 1.3e-108 349.0 0.0 1.0 1 NCBI__GCF_002165625.1:WP_087504727.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002165625.1:WP_087504727.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 349.0 0.0 1.3e-108 1.3e-108 1 315 [] 7 311 .. 7 311 .. 0.98 Alignments for each domain: == domain 1 score: 349.0 bits; conditional E-value: 1.3e-108 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrlt 73 l++d+GGtn rlalv+ e ++ y + ++p +++v+r ylee + ++++ +c+aia+P d++ +t NCBI__GCF_002165625.1:WP_087504727.1 7 LIADVGGTNIRLALVDEQGVEYTELRKYLCAQYPTITDVIRHYLEEVNASVRH---ACIAIACPTNSDWIDMT 76 79**************************************************9...***************** PP TIGR00749 74 nldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqs 146 n++Wa+s e+++el+l l +ind++a++++++ lk+++++q+g +e++a++a+lG+GtGlGva+l+ + NCBI__GCF_002165625.1:WP_087504727.1 77 NNSWAFSRREVQEELGLDALYIINDYTAISMSLPFLKDDQMVQVGPGMIEPAAPKAVLGPGTGLGVAHLVS-V 148 **********************************************************************9.* PP TIGR00749 147 dgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelk 219 +g++++l+geGghvdfaP ++ + +++yl k+y +vs e++lsG Gl++iyeal + +g e + NCBI__GCF_002165625.1:WP_087504727.1 149 EGHWHSLPGEGGHVDFAPIDDVDNYIWKYLNKRYPHVSYEQLLSGLGLIQIYEALCEMRGVTV------IERT 215 *******************************************************99985543......3568 PP TIGR00749 220 ekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrl 292 + di+ ++g++ l++ a+e f+ +lG+ agnla++lga+GGvyvaGGivPrf +++++s fra+fe kGr+ NCBI__GCF_002165625.1:WP_087504727.1 216 PADITTLGVAGECELCQAAVEQFCKVLGSHAGNLAMNLGAFGGVYVAGGIVPRFTDFVERSEFRARFEAKGRF 288 8************************************************************************ PP TIGR00749 293 kellasiPvqvvlkkkvGllGag 315 +++ +P ++ ++++GllGa+ NCBI__GCF_002165625.1:WP_087504727.1 289 TDYVRRVPTFLITEEQPGLLGAA 311 *********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (320 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: 13.49 // [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