Align glucokinase subunit (EC 2.7.1.1) (characterized)
to candidate WP_027699393.1 TT13_RS07430 ROK family glucokinase
Query= metacyc::MONOMER-6081 (323 letters) >NCBI__GCF_000691805.2:WP_027699393.1 Length = 325 Score = 399 bits (1026), Expect = e-116 Identities = 192/314 (61%), Positives = 244/314 (77%), Gaps = 1/314 (0%) Query: 4 KLLGIDLGGTSIKFGILTLDGQVQEKWAIETNILEDGKHIVPDIVSSIKHRLELYNLTKE 63 KL+GIDLGGT+IKF ILT++G++Q+KW++ TNIL++G HIVPDI+ SI H L+LY L +E Sbjct: 5 KLIGIDLGGTTIKFAILTVEGEIQQKWSLRTNILDEGTHIVPDIIESINHHLDLYQLDRE 64 Query: 64 DFVGIGMGSPGAVDRNLKTVTGAFNLNWAATQEVGTIIEAELGIPFAIDNDANVAALGER 123 +GIGMG+PG VD TV GAFNLNW+ Q V IE +P +DNDAN AALGE+ Sbjct: 65 RVLGIGMGTPGTVDIENGTVQGAFNLNWSNLQTVRQDIETATSLPLTLDNDANSAALGEQ 124 Query: 124 WVGAGNNNPDVVFVTLGTGVGGGIIADGNLIHGVAGAGGEIGHIIVEPDTGFECTCGNKG 183 W GAGNN P+VVF+TLGTGVGGG+I +G LIHG+ GA GE+GHIIV+P G++CTCGN G Sbjct: 125 WRGAGNNEPEVVFITLGTGVGGGLINEGKLIHGLNGAAGEVGHIIVQP-YGYQCTCGNYG 183 Query: 184 CLETVASATGVVRVARHLAEEYEGISSIKAGIDNGDDVSSKDIFVAAQAGDKFANSVVEK 243 CLE ASATGVV +A+ AEEY G S +KA IDNG++V+SK +F A+ D AN VV K Sbjct: 184 CLEQYASATGVVHLAQDFAEEYVGTSKLKAMIDNGEEVTSKIVFDLAKEDDYLANEVVNK 243 Query: 244 VTFYLGLATANISNILNPNTVVVGGGVSAAGEFLRSHIESYFKLYAFPQVKQSTKIKIAE 303 V +YLGLATANI+NILNP+++++GGGVSAAG FL ++ F +AF + +TK+K+AE Sbjct: 244 VAYYLGLATANIANILNPSSIIIGGGVSAAGNFLLERVQKNFFEFAFKTTRDATKVKLAE 303 Query: 304 LGNDAGIIGAASLA 317 LGNDAG+ GAASLA Sbjct: 304 LGNDAGVYGAASLA 317 Lambda K H 0.316 0.137 0.394 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: 347 Number of extensions: 8 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: 323 Length of database: 325 Length adjustment: 28 Effective length of query: 295 Effective length of database: 297 Effective search space: 87615 Effective search space used: 87615 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