Align Tagatose-6-phosphate kinase; EC 2.7.1.144; Phosphotagatokinase (uncharacterized)
to candidate N515DRAFT_0917 N515DRAFT_0917 tagatose 6-phosphate kinase
Query= curated2:Q833W9 (313 letters) >FitnessBrowser__Dyella79:N515DRAFT_0917 Length = 310 Score = 141 bits (356), Expect = 2e-38 Identities = 97/311 (31%), Positives = 152/311 (48%), Gaps = 7/311 (2%) Query: 1 MIVTVTMNPSIDISYLLDHLKLDTVNRTSQVTKTPGGKGLNVTRVIHDLGGDVIATGVLG 60 MI N +ID Y LD L+ V R + V PGGKGL+V + I LG V G+ Sbjct: 1 MITVAGFNTAIDRLYTLDALEPGAVQRAANVQAYPGGKGLHVAQTIAALGEPVQLVGLTD 60 Query: 61 GFHGAFIANELKKANIPQAFTSIKEETRDSIAILH-EGNQTEILEAGPTVSPEEISNFLE 119 FH IA + + + I E R +A+ +G TE+L+ GP + P L+ Sbjct: 61 VFHRNLIARRMSERGVLFHGVEIAGELRHCLALRERDGRMTEVLDPGPLLPPRAQQQLLD 120 Query: 120 NFDQLIKQAEIVTISGSLAKGLPSDFYQELVQKAHAQEVKVLLDTSGDSLRQVLQGPWKP 179 + ++ + + +SGSL +G +D Y L+++ + + L+D SG++LR L Sbjct: 121 TLWRCVEDTDAMVLSGSLPRGFEADTYAALLRQIAPRGLPCLVDASGEALR--LAADAGA 178 Query: 180 YLIKPNLEELEGLLGQDFSENPLAAVQTALTKPMFA-GIEWIVISLGKDGAIAKHHDQFY 238 +L+KPN +E L G+ AAV + + + A G+ + VI+LG GA+ + Sbjct: 179 FLLKPNRDEAAQLAGRAVDTVEDAAV---VARALHARGVAFPVITLGARGALGFDGADCW 235 Query: 239 RVKIPTIQAKNPVGSGDATIAGLAYGLAKDAPAAELLKWGMAAGMANAQERMTGHVDVEN 298 + + N VGSGD +AG A L + A+ L+ G+A G ANA TG+V Sbjct: 236 HASLAIAHSANAVGSGDCFLAGAAVALRRGGEPAQALRLGVACGAANALHEETGYVQRAQ 295 Query: 299 VKKHLMNIQVV 309 V L +++V Sbjct: 296 VDALLAEVRLV 306 Lambda K H 0.315 0.134 0.378 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: 202 Number of extensions: 12 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: 313 Length of database: 310 Length adjustment: 27 Effective length of query: 286 Effective length of database: 283 Effective search space: 80938 Effective search space used: 80938 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 17 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