Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_015820092.1 TERTU_RS14805 fructokinase
Query= BRENDA::Q8RDE9 (315 letters) >NCBI__GCF_000023025.1:WP_015820092.1 Length = 296 Score = 108 bits (270), Expect = 2e-28 Identities = 96/322 (29%), Positives = 146/322 (45%), Gaps = 56/322 (17%) Query: 7 GVDLGGTK----ISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGLEM 62 G++LGGTK I TG+ +I ++IPT P + +I + Sbjct: 8 GIELGGTKTICLIGTGV----DSIRDQLQIPTT---NPADTLGQIHTFL--------ASQ 52 Query: 63 SNLKGIGIGSPGPLN-----AKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANA 117 L GIGIG+ GP+N A G + S P P WS+ +V +R + L+ D NA Sbjct: 53 GELAGIGIGAFGPVNIDPGSANYGCIESTPK-PGWSHTSVVPFFRERFSCPINLDTDVNA 111 Query: 118 AAIGEHLFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINFDGPRCN 177 AAI EH G+G+G+ NF+YITV TGIGGG +IEG G ++ E+GH + PR Sbjct: 112 AAIAEHQHGNGKGLRNFIYITVGTGIGGGALIEGAPVRG--NSHPEMGHIAL----PR-- 163 Query: 178 CGNYGCFEAYASGTAIARFAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKLGDEFAKEL 237 + E + S + EG+ G + + E EH Sbjct: 164 ---HMADETFLSACPYHQNCAEGLASGSALRKRWGMPLNEFPPEH-------------PA 207 Query: 238 VEKEAFYLGVGIANIMAFYNPRKIAIGGGVSAQW------DMLYEKMMETVRKKALKPNA 291 + +A YL ++ ++P++I +GGGVS++ LY+K+ V L+ + Sbjct: 208 WDMQASYLAEFFHSLTLLFSPQRIIVGGGVSSEQLLARVRTALYKKLNGYVDALKLEASL 267 Query: 292 EVCEVVKAQLGENIGVLGAAAL 313 E + +L N G LG+ L Sbjct: 268 E-SYLCLPELAGNAGPLGSLML 288 Lambda K H 0.316 0.138 0.398 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: 228 Number of extensions: 14 Number of successful extensions: 4 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: 315 Length of database: 296 Length adjustment: 27 Effective length of query: 288 Effective length of database: 269 Effective search space: 77472 Effective search space used: 77472 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