Align hexokinase (EC 2.7.1.1) (characterized)
to candidate AZOBR_RS27950 AZOBR_RS27950 transcriptional regulator
Query= BRENDA::Q5RLG0 (302 letters) >FitnessBrowser__azobra:AZOBR_RS27950 Length = 392 Score = 160 bits (404), Expect = 6e-44 Identities = 99/246 (40%), Positives = 138/246 (56%), Gaps = 16/246 (6%) Query: 61 IGLGTPGPLDFRRGVIRFAPNIPGVQDFPIRRILEEATGRPVFLENDANAAALAEHHLGA 120 IG+G P +D R G + APN+ G +D PIR +LEEA G PV ++ND AAA+AE GA Sbjct: 149 IGVGIPALMD-REGRLVLAPNL-GWRDTPIRPLLEEALGAPVHVDNDTKAAAMAERLFGA 206 Query: 121 AQGEESSLYLTVSTGIGGGVVLGGRVLRGERGQGGELGHLTLLPGGPACGCGLEGCLEAL 180 +G E +YLT +G+GGG+ GGR+ RG +G GE+GHLT++PGG ACGCG GCLE Sbjct: 207 CRGVEDFVYLTGHSGVGGGLFFGGRLYRGAQGFAGEIGHLTIVPGGRACGCGKRGCLETY 266 Query: 181 AAGRALERDATYAFQCPVDTRELFRLFQAGDPKAERLVLQAARYVGIGLASLVKAFDPGV 240 + ++ A + D + GDP L+ +A ++G L+ LV +PG+ Sbjct: 267 VSETSILAQAAERGRALPDLWAAAAAARDGDPVVRTLLEEAGSHLGFALSHLVNLANPGL 326 Query: 241 VVLGGGVALNAPEGYWEALLEAYRRYLQGWEAPPLRR------ARLGAEA---GLLGAAL 291 VVLGG +A+ A E +L A L PLRR + LG +A G + A+ Sbjct: 327 VVLGGNLAIVA-----EFILPALNAALGEHALEPLRRDLRLLVSPLGPDAVPMGGIALAM 381 Query: 292 TAYLEV 297 +L V Sbjct: 382 DGFLSV 387 Lambda K H 0.319 0.141 0.416 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: 188 Number of extensions: 5 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: 392 Length adjustment: 29 Effective length of query: 273 Effective length of database: 363 Effective search space: 99099 Effective search space used: 99099 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