Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_013430999.1 CALKRO_RS10530 ROK family protein
Query= BRENDA::Q8R8N4 (312 letters) >NCBI__GCF_000166775.1:WP_013430999.1 Length = 316 Score = 329 bits (844), Expect = 5e-95 Identities = 164/310 (52%), Positives = 218/310 (70%) Query: 3 IGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVKDV 62 IG+DLGGTNIA G+V+E GKII GS PT R Y I +D+AELS L++ G+++ D+ Sbjct: 4 IGIDLGGTNIAAGIVDEGGKIIKKGSVPTGAHRHYTEIMKDMAELSLNLVKECGLTLDDI 63 Query: 63 KSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDANVAALAEATFG 122 S+GIG PG DNEKG+++ + N+ + VP+ +EI+KYI P+ +ENDAN AA E G Sbjct: 64 HSVGIGSPGAPDNEKGMILYSNNIAFLNVPMREEIQKYIPKPVNIENDANCAAYGEYIAG 123 Query: 123 AGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGCFET 182 +G+K SVTITLGTG+G G I+DGKI++GAHH E+GHMVI +G +C CG+ GC+E Sbjct: 124 GAKGTKISVTITLGTGIGGGIIIDGKIFTGAHHAGAELGHMVICVDGEQCTCGRRGCWEA 183 Query: 183 YASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFEEYVKY 242 YASATALIR ++AA R+ N I+K NGDI I AK DA + D I + YVKY Sbjct: 184 YASATALIRMTREAAARDINGTIMKLVNGDISKIDAKTAFDAKRMGDSTGAAIVDRYVKY 243 Query: 243 LAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRKAELGND 302 LA G+ NI N+F+PEVI +GGGV+ G++LL+P++K V E K++P I A LGND Sbjct: 244 LAEGLANICNIFEPEVICIGGGVSKEGEYLLEPVRKLVYEKFYCKQVPMPKIIPAVLGND 303 Query: 303 AGIIGAAILS 312 AGIIGAA+L+ Sbjct: 304 AGIIGAALLA 313 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: 363 Number of extensions: 19 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: 312 Length of database: 316 Length adjustment: 27 Effective length of query: 285 Effective length of database: 289 Effective search space: 82365 Effective search space used: 82365 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