Align hexokinase (EC 2.7.1.1) (characterized)
to candidate WP_011612072.1 TERY_RS11945 ATPase
Query= BRENDA::Q96Y14 (299 letters) >NCBI__GCF_000014265.1:WP_011612072.1 Length = 322 Score = 120 bits (301), Expect = 4e-32 Identities = 95/318 (29%), Positives = 150/318 (47%), Gaps = 40/318 (12%) Query: 4 IVGVDAGGTKTKAVAYDCEGNFIGEGSSGPGNYHNVGLTRAIENIKEAVKIAAKGEADV- 62 ++G+D GGTKT+AV D +G G SGP NYH+VG+ A +I+ A+ A Sbjct: 6 VLGIDGGGTKTEAVLMDENCQVLGSGKSGPSNYHSVGIEVAKNSIQTAITQAVANSNSYQ 65 Query: 63 ----VGMGVAGLDSKFDWENFTPLASLIAP--------------KVIIQHDGVIALFAET 104 + +G+AG+ E+F + SL+ V+I D IAL Sbjct: 66 PISGICLGLAGVGRP---EDFLVVESLLKEIMMDIPIKWDLQPNTVVICSDSNIALVGGL 122 Query: 105 LGEPGVVVIAGTGSVVEGYNGKEFL-RVGGRGWLLSDDGSAYWVGRKALRKVLKMMDGLE 163 G+V IAGTGS+V G N RVGG G+LL D+GS Y + + L+ LK DG E Sbjct: 123 GCSVGIVAIAGTGSLVFGQNSHGLTKRVGGWGYLLGDEGSGYNIAIRGLQAALKSYDGRE 182 Query: 164 NKTILYNKVLKTINVKDLDELVMWSYTSSCQIDLVASIAKAVDEAANEGDTVAMDILKQG 223 + TIL + + +K+++ ++ Y + +A++A V AA++ D VA I++ Sbjct: 183 SPTILVTDFTRYLGLKNIEGIIEIIYRRRWDVTRIAALAPIVSAAADKEDKVAKKIIQGA 242 Query: 224 AELLASQAVYLARKIGTNKVYLKGGMFR----SNIYHKFFTLYLEKEGIISDLG------ 273 E L+ A KI + ++ +F ++++ + E I+ + Sbjct: 243 VEELSK-----ATKIVISTLFQVHEIFEVVTIGSVWNSMINFRGQFEDSIAAIAPTAQVI 297 Query: 274 --KRSPEIGAVILAYKEV 289 K P GA ILA K + Sbjct: 298 WPKHEPVYGAAILALKAI 315 Lambda K H 0.317 0.137 0.395 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: 243 Number of extensions: 8 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: 299 Length of database: 322 Length adjustment: 27 Effective length of query: 272 Effective length of database: 295 Effective search space: 80240 Effective search space used: 80240 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