Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate N515DRAFT_0916 N515DRAFT_0916 Sugar or nucleoside kinase, ribokinase family
Query= metacyc::MONOMER-12748 (320 letters) >FitnessBrowser__Dyella79:N515DRAFT_0916 Length = 312 Score = 72.0 bits (175), Expect = 2e-17 Identities = 77/258 (29%), Positives = 109/258 (42%), Gaps = 18/258 (6%) Query: 42 AIGLARLGFKVAWLSRVGNDSLGRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGD 101 A+GLARLG VA+ R+G D+ G + LD LR G+D ++ + TG + S D Sbjct: 51 AMGLARLGNAVAFHGRLGADAWGSYCLDALRDAGIDVASLQPEAALRTGITV-SLSTPRD 109 Query: 102 DPRVEYFRRGSAASHLAISDLDPALLR-ARHLHATGIPPALSDSARELSGHLMHTQRSAG 160 V + A + L D+ ALL A HLH + L + R L R AG Sbjct: 110 RSLVTF---SGAIAALRAEDVSDALLAGAGHLHVSSF--YLQKALRADIRQLFARARKAG 164 Query: 161 HSVSFDPNLRPALWPSEALMIREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQ 220 ++S DP P E ++ + LP E R LTG + A LD Sbjct: 165 LTLSLDPGFDP-----EQRWGDDLRGVLEDVDVFLPNEEELRALTGENHVRKALA-ALDN 218 Query: 221 GAEAVVIKLGAHGAYYRTQLDAGFVEGVP--VAQVVDTVGAGDGFAVGLISALLESRGIL 278 G +V K G G L G + P + VD+ GAGD F G + A L + Sbjct: 219 GRTLIVAKRGRQGC---AVLHDGKLLVAPALAVEAVDSTGAGDSFDAGFLHAWLRGLPLR 275 Query: 279 EAVQRANWIGSRAVQSRG 296 + ++ N GS + + G Sbjct: 276 DCLRWGNACGSLSTRGIG 293 Lambda K H 0.321 0.138 0.414 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: 254 Number of extensions: 22 Number of successful extensions: 2 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: 320 Length of database: 312 Length adjustment: 27 Effective length of query: 293 Effective length of database: 285 Effective search space: 83505 Effective search space used: 83505 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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