Align Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized)
to candidate WP_013430927.1 CALKRO_RS10160 ROK family transcriptional regulator
Query= SwissProt::Q9X1I0 (317 letters) >NCBI__GCF_000166775.1:WP_013430927.1 Length = 399 Score = 144 bits (363), Expect = 4e-39 Identities = 93/317 (29%), Positives = 158/317 (49%), Gaps = 19/317 (5%) Query: 6 LIGVDLGGTTFSVGLVSEDGKILKKVTRDTLVENGKEDVIRRIAETILEVSDGEEAPY-- 63 +IG+DLG V L + G+++ + + + K+ + + + I + D AP+ Sbjct: 80 IIGIDLGVDYIHVILSNFVGEVIFEEYAEMKMGEDKDKLFDLLFDLIEKAID--RAPHTP 137 Query: 64 -----VGIGSPGSIDRENGIVRFSPNFPDWHNVPLTDELAKRTGKKVFLENDANAFVLGE 118 +GIG PG +++E+GIV +PN W NV L + +R V+++N+ANA LGE Sbjct: 138 KGILGIGIGVPGIVEKESGIVLIAPNLK-WKNVHLKSIVQQRFNLPVYIDNEANAGALGE 196 Query: 119 KWFGAGRGHDHIVALTLGTGIGGGVVTHGYLLTGRDGIGAELGHVVVEPNGPMCNCGTRG 178 KWFG ++ L++G G+G G++ L G G E+GH + +C+CG G Sbjct: 197 KWFGEWGKVSDLIYLSVGIGLGAGIIIDNKLFRGAAGFAGEVGHTTINFQDDVCSCGNIG 256 Query: 179 CLEAVASATA----IRRFLREGYKKYHSSLVYKLAGSPEKADAKHLFDAARQGDRFALMI 234 CLE AS A I++ +++G + + S + + + AA++G R M Sbjct: 257 CLENFASERALLSVIKKLVKQGVEDRYIS-----CENVHEITPSRIIQAAKEGSRVCRMA 311 Query: 235 RDRVVDALARAVAGYIHIFNPEIVIIGGGISRAGEILFGPLREKVVDYIMPSFVGTYEVV 294 V + + VA ++IFNPE+VIIG S GE+ LRE + + ++ Sbjct: 312 ILEVAEKMGIGVANLVNIFNPEMVIIGNKASFFGELFLEKLREVINQRSFIAQFYNLKIE 371 Query: 295 ASPLVEDAGILGAASII 311 S L + A +LG +++ Sbjct: 372 VSKLKDRAVVLGCIAMV 388 Lambda K H 0.320 0.142 0.418 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: 311 Number of extensions: 14 Number of successful extensions: 3 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: 317 Length of database: 399 Length adjustment: 29 Effective length of query: 288 Effective length of database: 370 Effective search space: 106560 Effective search space used: 106560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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