Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_167332675.1 RHSP_RS25550 ROK family protein
Query= BRENDA::Q8RDE9 (315 letters) >NCBI__GCF_000359745.1:WP_167332675.1 Length = 395 Score = 134 bits (336), Expect = 5e-36 Identities = 99/310 (31%), Positives = 146/310 (47%), Gaps = 22/310 (7%) Query: 7 GVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGLEM-SNL 65 GV++G T + T ++D +G K P DV E++ + + + L Sbjct: 89 GVEMGSTHMVTTVLDLSGKPRKQHVRPIH-----DVSSEKLSAQLRAEVDAVRTSFPARL 143 Query: 66 KGIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAAIGEHLF 125 GIG+ PGP + + + P LP WS + E+LS+ G V +ENDANAAA+GE LF Sbjct: 144 LGIGVVMPGPFDIEGMSSVGPTTLPGWSGIDAAEVLSEACGEPVLVENDANAAAVGERLF 203 Query: 126 GSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINFDGPRCNCGNYGCFE 185 G+G + NF I GIG G+I +G + G NA EIGH I +G RC CG GC E Sbjct: 204 GAGHAISNFAMIYFGAGIGLGMIQDGAPFRGAFGNAGEIGHIVITPNGRRCACGQKGCLE 263 Query: 186 AYASGTAI-ARFAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKLGDEFAKELVEKEAFY 244 YAS A+ + GIE +++L GE + + ++ A + Sbjct: 264 TYASLHALREKLHAAGIENTDFDALEKLHGE--------------RNPVVIDWLQDAADH 309 Query: 245 LGVGIANIMAFYNPRKIAIGGGVSAQ-WDMLYEKMMETVRKKALKPNAEVCEVVKAQLGE 303 L IA I +P + +GG + + D L M E A + + V++ Q G+ Sbjct: 310 LAPMIAMIENILDPETVIMGGMLPDEIIDDLIRHMGELPISVASRRARALPRVLRGQTGK 369 Query: 304 NIGVLGAAAL 313 LGAA+L Sbjct: 370 FTAALGAASL 379 Lambda K H 0.316 0.138 0.398 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: 316 Number of extensions: 12 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: 315 Length of database: 395 Length adjustment: 29 Effective length of query: 286 Effective length of database: 366 Effective search space: 104676 Effective search space used: 104676 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: 49 (23.5 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