Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_158665540.1 C3B54_RS04755 ROK family protein
Query= BRENDA::P0A4E1 (317 letters) >NCBI__GCF_002950575.1:WP_158665540.1 Length = 300 Score = 180 bits (457), Expect = 3e-50 Identities = 113/316 (35%), Positives = 169/316 (53%), Gaps = 28/316 (8%) Query: 4 TIGVDIGGTKIAAGVVDEEGNILSTHKVPTPTTPEAIVDAIASAVEGARVGHEIVAVGIG 63 ++G+DIGGT I AG+V G +VPTP+ P+AI+D + + V VG+ Sbjct: 3 SLGIDIGGTSIKAGIVGPRGLEGEIRQVPTPSHPDAIIDTTLALAKSFPVQP---TVGVA 59 Query: 64 AAGYVNRQRSTVYFAPNIDWRQEPLKEKVEARVGLPVVVENDANAAAWGEYKFGGGKGHR 123 A +++ R+ V F+PNI W PL+ ++E + LPVV+ENDANAA +GEY G G+ Sbjct: 60 VAAFLDPARTHVEFSPNIAWDGRPLRHELEEGLQLPVVLENDANAAGYGEYVLGAGQQAS 119 Query: 124 NVICITLGTGLGGGIIIGNKLRRGHFGVAAEFGHIRMVPDGLLCGCGSQGCWEQYASGRA 183 ++ +TLGTG+GG +I+ KL G GVA E GHI + P G +CGCG +GC E +SG A Sbjct: 120 PMVMLTLGTGVGGAVILDGKLLAGARGVAGELGHIVVNPGGAVCGCGQRGCVETVSSGTA 179 Query: 184 LVRYAKQRANATPERAEVLLALGDGTPDGIEGKHISVAARQGCPVAVDSYRELARWAGAG 243 L+ A+Q ALG I H A +Q A + + L G Sbjct: 180 LMTMARQ-------------ALG----IEINSTH---ALKQALVDAPELRKTLLNTMAEG 219 Query: 244 ----LADLASLFDPSAFIVGGGLSDE-GDLVLDPIRKSYKRWLVGGNWRPVADVIAAQLG 298 L + ++ DP+ ++GGG+++ G + D + + L G ++ A+LG Sbjct: 220 IIGALLQIQAVVDPALSVIGGGVTERLGAELFDALDRLKDDALDGRRSVAFPPIVPAELG 279 Query: 299 NKAGLVGAADLAREPD 314 N AG++GA LA+ D Sbjct: 280 NSAGIIGAGLLAQRHD 295 Lambda K H 0.318 0.139 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: 341 Number of extensions: 19 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: 317 Length of database: 300 Length adjustment: 27 Effective length of query: 290 Effective length of database: 273 Effective search space: 79170 Effective search space used: 79170 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
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