Align hexokinase (EC 2.7.1.1) (characterized)
to candidate WP_012756919.1 RLEG_RS06410 ROK family transcriptional regulator
Query= BRENDA::Q5SLJ4 (302 letters) >NCBI__GCF_000023185.1:WP_012756919.1 Length = 393 Score = 129 bits (324), Expect = 1e-34 Identities = 94/297 (31%), Positives = 140/297 (47%), Gaps = 23/297 (7%) Query: 4 VGLDLGGTKIAAGVFDGKRLLSKVV----VPTPKEGGERVAEALAEAAERAEREAGVRGE 59 V +DLG TKIAA + D LL VV VPT GG + ++ AG + Sbjct: 87 VSIDLGSTKIAAAICD---LLGNVVAETKVPTDPRGGVHLVNQFSDLIVELAFAAGTTAD 143 Query: 60 AIGL---GTPGPLDFRRGVIRFAPNIPGVQDFPIRRILEEATGRPVFLENDANAAALAEH 116 + L G+PG LD G I AP+IPG+ +R++ + G PV +END N AA E Sbjct: 144 KLRLVVLGSPGVLDPATGHINVAPSIPGIDAINLRQVFSDRMGIPVIVENDVNLAAQGER 203 Query: 117 HLGAAQGEESSLYLTVSTGIGGGVVLGGRVLRGERGQGGELGHLTLLPGGPAC---GCGL 173 G + ++ + TG+G G++ G +LRG RG GE+ +L + GG A G L Sbjct: 204 WRGHGIETSNFAFVALGTGVGMGIIANGTLLRGARGAAGEIAYLPI--GGDAFDPGGFTL 261 Query: 174 EGCLEALAAGRALERDATYAFQRPVDTRELFRLFQAGDPKAERLVLQAARYVGIGLASLV 233 A+ + L R + + +LF F AG+ A + + AR V + +A++ Sbjct: 262 GTFESAVGSVAMLRRYVGFGGRNASTVADLFAAFNAGETSAAAAIEETARLVAVAIAAIG 321 Query: 234 KAFDPGVVVLGGGVALNAPEGYWEALLEAYRRYLQGWE--APPLRRARLGAEAGLLG 288 A DP +V+ GG + G L+ A R +L P + +R G A L+G Sbjct: 322 AALDPELVITGGSI------GARLELVNAIRGFLPRCTPYPPRIEISRFGNRAALMG 372 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: 172 Number of extensions: 6 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: 302 Length of database: 393 Length adjustment: 29 Effective length of query: 273 Effective length of database: 364 Effective search space: 99372 Effective search space used: 99372 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