Align Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized)
to candidate Synpcc7942_2111 Synpcc7942_2111 xylose repressor
Query= SwissProt::Q9X1I0 (317 letters) >FitnessBrowser__SynE:Synpcc7942_2111 Length = 302 Score = 181 bits (460), Expect = 1e-50 Identities = 107/310 (34%), Positives = 159/310 (51%), Gaps = 20/310 (6%) Query: 6 LIGVDLGGTTFSVGLVSEDGKILKKVTRDTLVENGKEDVIRRIAETILEVSDGEEAPYVG 65 +IGVDLGGT +G + +G+ +++T T + +V + E I ++ EA +G Sbjct: 7 VIGVDLGGTAMKLGRYTIEGQCQQELTVPTPTPSTPSNVRAALVEAIRQLDPQAEALAIG 66 Query: 66 IGSPGSIDRENGIVRFSPNFPDWHNVPLTDELAKRTGKKVFLENDANAFVLGEKWFGAGR 125 IG+PG D + R + N W VPL D L + V L NDAN LGE W G GR Sbjct: 67 IGTPGPADAAGRVARVAINLDGWTEVPLADWLEADLQRPVILANDANCAGLGEVWLGGGR 126 Query: 126 GHDHIVALTLGTGIGGGVVTHGYLLTGRDGIGAELGHVVVEPNGPMCNCGTRGCLEAVAS 185 G+ + LTLGTG+GG +V +G L GR G AELG + ++P GP CN G +G LE AS Sbjct: 127 GYRDAILLTLGTGVGGAIVLNGELFVGRTGTAAELGLITLDPAGPHCNSGNQGSLEQYAS 186 Query: 186 ATAIRRFLREGYKKYHSSLVYKLAGSPEKADAKHLFDAARQGDRFALMIRDRVVDALARA 245 A++R R G D K L D A QGD A+ LA Sbjct: 187 IGAVQR--RFG------------------CDPKDLGDRASQGDPEAIAAWQDYGRTLAAG 226 Query: 246 VAGYIHIFNPEIVIIGGGISRAGEILFGPLREKVVDYIMPSFVGTYEVVASPLVEDAGIL 305 +A +++ PE++I+GGGIS + L E++ ++P+ ++ + L +AG + Sbjct: 227 LASLVYVLTPEVIILGGGISGSAAFFLPALTEELHRRVLPTSREDLQIAIAALGNEAGRV 286 Query: 306 GAASIIKERI 315 GAA + +++ Sbjct: 287 GAAKLAWDKL 296 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: 213 Number of extensions: 10 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: 317 Length of database: 302 Length adjustment: 27 Effective length of query: 290 Effective length of database: 275 Effective search space: 79750 Effective search space used: 79750 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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