Align hexokinase (EC 2.7.1.1) (characterized)
to candidate WP_004110897.1 RHSP_RS06555 ROK family transcriptional regulator
Query= BRENDA::Q5RLG0 (302 letters) >NCBI__GCF_000359745.1:WP_004110897.1 Length = 408 Score = 109 bits (272), Expect = 1e-28 Identities = 93/306 (30%), Positives = 140/306 (45%), Gaps = 30/306 (9%) Query: 4 VGLDLGGTKIAAGVFDG------KRLLSKVVVPTPKEGGERVAEALAEAAERAEREAGVR 57 +GL+LG + AAGV R+ V P P E A + + E + R Sbjct: 86 IGLELGRQR-AAGVLTDLSGTVCARIDRHVDRPGPTEAMPVFAAIVRDLQEAFSFD---R 141 Query: 58 GEAIGLGTPGPLDFRRG-VIRFAP-NIPGVQDFPIRRILEEATGRPVFLENDANAAALAE 115 +G+G P + G V +P N+PG Q+FP+ R LE G PV +ENDA A A+ E Sbjct: 142 DRLLGVGIALPGRYADGGVTSLSPLNLPGWQNFPVARELERLIGLPVLVENDATAGAIGE 201 Query: 116 HHLGAAQGEESSLYLTVS--TGIGGGVVLGGRVLRGERGQGGELGHLTLLPGGPACGCGL 173 G A+G S +YL ++ GIG G+ L G + +G R GE+GH+ + P G C CG Sbjct: 202 RLYGVARGLGSFVYLFLAGDGGIGAGMFLDGHLYKGSRANAGEIGHIIVEPHGRLCTCGK 261 Query: 174 EGCLEALAAGRALERDATYAFQC-------PVDTRELFRLFQAGDPKAERLVLQAARYVG 226 GCL+ + + A++C +D +L + A + + QA + + Sbjct: 262 RGCLDRYVS-------PSVAYECLGIEDAQELDPDDLDAMIAANSRGLQTWLEQAVQPLR 314 Query: 227 IGLASLVKAFDPGVVVLGGGVALNAPEGYWEAL--LEAYRRYLQGWEAPPLRRARLGAEA 284 + L AFDP +VLGG + G E + L ++ + P L G + Sbjct: 315 QTIDFLELAFDPQTIVLGGSAPPSLMTGLAERVEPLHIPVNPMEERKIPRLMVGATGKDT 374 Query: 285 GLLGAA 290 +LGAA Sbjct: 375 AILGAA 380 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: 192 Number of extensions: 12 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 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