Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_013430927.1 CALKRO_RS10160 ROK family transcriptional regulator
Query= BRENDA::Q8R8N4 (312 letters) >NCBI__GCF_000166775.1:WP_013430927.1 Length = 399 Score = 164 bits (414), Expect = 4e-45 Identities = 93/305 (30%), Positives = 158/305 (51%), Gaps = 2/305 (0%) Query: 3 IGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVKDV 62 IG+DLG I V L G++I K + + + +L + + R + K + Sbjct: 81 IGIDLGVDYIHVILSNFVGEVIFEEYAEMKMGEDKDKLFDLLFDLIEKAIDRAPHTPKGI 140 Query: 63 KSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDANVAALAEATFG 122 +GIGVPG+ + E GIV+ A NL W V L +++ +LP+Y++N+AN AL E FG Sbjct: 141 LGIGIGVPGIVEKESGIVLIAPNLKWKNVHLKSIVQQRFNLPVYIDNEANAGALGEKWFG 200 Query: 123 AGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGCFET 182 + +++G G+G+G I+D K++ GA FA E+GH I C+CG IGC E Sbjct: 201 EWGKVSDLIYLSVGIGLGAGIIIDNKLFRGAAGFAGEVGHTTINFQDDVCSCGNIGCLEN 260 Query: 183 YASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFEEYVKY 242 +AS AL+ KK K+ + N + IT +I AAK+ E + Sbjct: 261 FASERALLSVIKKLVKQGVEDRYISCEN--VHEITPSRIIQAAKEGSRVCRMAILEVAEK 318 Query: 243 LAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRKAELGND 302 + +G+ N++N+F+PE++I+G + G+ L+ L++ + + + I ++L + Sbjct: 319 MGIGVANLVNIFNPEMVIIGNKASFFGELFLEKLREVINQRSFIAQFYNLKIEVSKLKDR 378 Query: 303 AGIIG 307 A ++G Sbjct: 379 AVVLG 383 Lambda K H 0.318 0.140 0.397 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: 350 Number of extensions: 19 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: 312 Length of database: 399 Length adjustment: 29 Effective length of query: 283 Effective length of database: 370 Effective search space: 104710 Effective search space used: 104710 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: 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