Align hexokinase (EC 2.7.1.1) (characterized)
to candidate SMa2303 SMa2303 ROK family transcriptional regulator
Query= BRENDA::Q5SLJ4 (302 letters) >FitnessBrowser__Smeli:SMa2303 Length = 408 Score = 112 bits (279), Expect = 2e-29 Identities = 83/261 (31%), Positives = 127/261 (48%), Gaps = 16/261 (6%) Query: 24 LSKVVVPTPKEGGERVAEALAEAAER----AEREAGVRGEAIGLGTPGPLDFRRGVIRFA 79 L+ + +P P + +AEALA AA + A R A R IG+ PG +D +R V Sbjct: 124 LASLRLPLPAHDPDTIAEALAAAAPKLVALANRPAA-RLAGIGIAMPGVIDNQRAVC-IR 181 Query: 80 PNIPGVQDFPIRRILEEATGRPVFLENDANAAALAEHHLGAAQGEESSLYLTVSTGIGGG 139 N G + P+ ++ G PV+LE+D NA A+A+ G + ++ L + G+ Sbjct: 182 SNRYGWDNVPLGDLVASRIGVPVWLEDDTNAYAIAQQLFGLGRHYKTMGVLAIGVGVACS 241 Query: 140 VVLGGRVLRGERGQGGELGHLTLLPGGPACGCGLEGCLEALAAGRALERDATYAFQRP-V 198 +VL G++ RG G G+ GH + GG C CG GCL + + A+ + RP Sbjct: 242 LVLDGKLYRGAHGAAGKFGHFPHMEGGRPCECGKRGCLMSYFSEPAMLQTWHERSGRPET 301 Query: 199 DTR-ELFRLFQAGDPKAERLVLQAARYVGIGLASLVKAFDPGVVVLGGGVALNAPEGYWE 257 D R E+ AGD A ++ +A +G LA L+ DP V+V+GG Y + Sbjct: 302 DGRAEMVAAIAAGDKAAHSVMREAGETLGRHLAGLMNVIDPEVIVVGGEAV-----AYGD 356 Query: 258 ALLEAYRRYLQGW---EAPPL 275 AL R L+ + +APP+ Sbjct: 357 ALFGPLRATLERFAFRQAPPV 377 Lambda K H 0.318 0.141 0.414 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: 171 Number of extensions: 9 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: 302 Length of database: 408 Length adjustment: 29 Effective length of query: 273 Effective length of database: 379 Effective search space: 103467 Effective search space used: 103467 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 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