Align hexokinase (EC 2.7.1.1) (characterized)
to candidate WP_049991158.1 LT39_RS14210 ROK family protein
Query= BRENDA::Q7ZAH1 (301 letters) >NCBI__GCF_000784335.1:WP_049991158.1 Length = 325 Score = 144 bits (364), Expect = 2e-39 Identities = 102/309 (33%), Positives = 148/309 (47%), Gaps = 28/309 (9%) Query: 5 IDVGATWTRVLLVSRDGRVERREKFRTDESP--------VEKAARLVEGW------EFEA 50 +D+GAT R ++ DG + T P V + R G A Sbjct: 7 VDLGATNVRAVVAEADGTTIGVSRRSTPRGPTGIDVTEGVLRTLRQACGEAGIAPDRIAA 66 Query: 51 IGVGSIGPMDLRRGWVTASPNSPSK--SFPLVEPLLKF--KRPVYVANDCVAAAWGEYVL 106 G+GSIGP DL G V N P+ PL P+ K VY+ ND A GE Sbjct: 67 AGIGSIGPFDLAEGAVIDPANLPNSIDRIPLTGPIGKLIDSDEVYLHNDTTAGVIGERFH 126 Query: 107 GGWGVDNLAYLTLSTGLGVGAVVNGHLILGKEGNAHELGHAVLDVRGDVKCGCGGLGHWE 166 D++ Y+T+S+G+G G +G ++ G +GNA E+GH V+D RG + CGCG GHWE Sbjct: 127 ADRNPDDMVYITISSGIGAGVCCDGEIMGGWDGNAGEVGHYVVDPRGRLTCGCGREGHWE 186 Query: 167 AMAGGANIPSYFRVFA-------ARLGLRAPEVRTAEDVFKLYREGDRVAQMFVDHWVDV 219 A G IP Y ++ A L L + TA+DVF+L E D +A ++ Sbjct: 187 AYCSGNAIPDYAKLLAEDDPTISTNLPLNGSDF-TAKDVFELAGE-DELADYVIEQLAHW 244 Query: 220 NAAGIATITAAYDPEVLVVGGSIALNHWDLVEAAV-DRLKKYTPLTPPALEKAKFGDDEV 278 NA G+ + A+ P V+ GG++AL++ +LV + +R+ + P + GDD V Sbjct: 245 NAIGVTNVIHAFAPIVVSFGGAVALHNEELVVDPIRERVSEMVMTNVPEIRVTDLGDDVV 304 Query: 279 AMGAAALAI 287 GA A A+ Sbjct: 305 LEGALASAL 313 Lambda K H 0.320 0.139 0.433 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: 303 Number of extensions: 24 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: 301 Length of database: 325 Length adjustment: 27 Effective length of query: 274 Effective length of database: 298 Effective search space: 81652 Effective search space used: 81652 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 (21.8 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