Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_004325323.1 C665_RS17905 ROK family protein
Query= reanno::SB2B:6937235 (310 letters) >NCBI__GCF_000310185.1:WP_004325323.1 Length = 301 Score = 304 bits (778), Expect = 2e-87 Identities = 151/295 (51%), Positives = 198/295 (67%), Gaps = 1/295 (0%) Query: 3 RSGIDLGGTKIELVTLNEKGEEVFRKRVPTPK-DYRATLEAVAGLVHDSEKETGQVSSVG 61 R GIDLGGTKIELV L+ G E +R+RVPTP+ DY TL A+A LV ++E+ TG + +G Sbjct: 4 RIGIDLGGTKIELVVLDADGRERWRRRVPTPQGDYGGTLRAIAALVEEAERLTGAGARIG 63 Query: 62 IGIPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAG 121 +G PG S GR++N+N+ LNGQP+ +DL A+L R +R+ANDANC A+SE+ DG GAG Sbjct: 64 VGTPGSPSPRDGRIRNANSTCLNGQPLQQDLEALLRRPLRLANDANCLAMSEAADGAGAG 123 Query: 122 KTLVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLPWMTADEFNSTRCFCGNADCI 181 VF AILGTG G GI ++ K+ G N + GEWGHNPLP D+ C+CG A CI Sbjct: 124 ARTVFAAILGTGVGGGIVVDQKLLVGANAVAGEWGHNPLPLPAPDDLPLPACYCGRAGCI 183 Query: 182 ETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVINLLD 241 ET++SG G D HGGE I +G+ ++A+ R+ RLARALA VINLLD Sbjct: 184 ETYLSGPGLAADHLRHGGEPLDAAAIARQATEGQRASQASLERYELRLARALAGVINLLD 243 Query: 242 PDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWLW 296 P+VIVLGGG+S I +YE++P +V +T+++ HG +SGVRGAAWLW Sbjct: 244 PEVIVLGGGLSQIARLYEHVPRRWAAHVFSDTVSTRLLPARHGDASGVRGAAWLW 298 Lambda K H 0.318 0.138 0.424 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: 333 Number of extensions: 12 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: 310 Length of database: 301 Length adjustment: 27 Effective length of query: 283 Effective length of database: 274 Effective search space: 77542 Effective search space used: 77542 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 (21.6 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