Align hexokinase (EC 2.7.1.1) (characterized)
to candidate WP_015817972.1 TERTU_RS03515 ATPase
Query= BRENDA::Q96Y14 (299 letters) >NCBI__GCF_000023025.1:WP_015817972.1 Length = 299 Score = 101 bits (252), Expect = 2e-26 Identities = 95/306 (31%), Positives = 144/306 (47%), Gaps = 43/306 (14%) Query: 3 IIVGVDAGGTKTKAVAYDCEGNFIGEGSSGPGNYHNVGLTRAIENIKEAVKIAAK----- 57 + +GVD GGTK +AV D + N IG+G G N + +AI++I A + A Sbjct: 11 LFMGVDGGGTKCRAVLVDGQKNVIGQGEGGACNAYQ-SFDKAIDSILVASEKALMEAGLK 69 Query: 58 -GEAD--VVGMGVAGLDSK------FDWENFTPLASLIAPKVIIQHDGVIALFAETLGEP 108 G+ D VVGMG+AG++ ++W++ L+ D A A G Sbjct: 70 AGDRDKVVVGMGLAGVNIPDVYTRVWNWQHPFKARFLMT-------DLHAACVAAHGGSE 122 Query: 109 GVVVIAGTGSVVEGYNGKEFLRVGGRGWLLSDDGSAYWVGRKALRKVLKMMDGLENKTIL 168 G V++AGTGS G L++G G+ D GS W+G +AL+ VL D L T+L Sbjct: 123 GAVIVAGTGSCGFAQAGDRVLKLGAHGFPFGDKGSGAWIGLQALQAVLLNFDDLGKPTML 182 Query: 169 YNKVLKTINVKDLDELVMWSYTSSCQIDLVASIAKAVDEAANEGDTVAMDILKQGAELLA 228 + + LD + + + AS+A AV AA GD+VA+ IL++GA+ L+ Sbjct: 183 TELIASELKADGLDII---ERMHNARTGDYASLAPAVFTAAEAGDSVAIAILREGADYLS 239 Query: 229 SQAVYLARKIGTNKVYLKGGMFRSNIYHKFFTLYLEKEGIISDLGKR------SPEIGAV 282 A L I ++ + GG I HK K+ + D+ +R PE GA+ Sbjct: 240 DLADRL-WSINPPRMSMLGG-----ISHKM------KDWMRKDIIERMSPALQQPEHGAL 287 Query: 283 ILAYKE 288 A +E Sbjct: 288 FYAMQE 293 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: 265 Number of extensions: 20 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: 299 Length adjustment: 27 Effective length of query: 272 Effective length of database: 272 Effective search space: 73984 Effective search space used: 73984 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