Align 5-dehydro-2-deoxygluconokinase 1; EC 2.7.1.92; 2-deoxy-5-keto-D-gluconate kinase 1; DKG kinase 1 (uncharacterized)
to candidate BPHYT_RS11300 BPHYT_RS11300 2-dehydro-3-deoxygluconokinase
Query= curated2:Q63B75 (332 letters) >FitnessBrowser__BFirm:BPHYT_RS11300 Length = 327 Score = 118 bits (295), Expect = 2e-31 Identities = 93/324 (28%), Positives = 149/324 (45%), Gaps = 8/324 (2%) Query: 7 KENRPFDLIAVGRLCVDLNANETQRPMEETRTFTKYVGGSPANIAIGAARLGLQTGFIGK 66 K D+I G A ET P+ FTK V G+ N+AIG +RLG + G++ + Sbjct: 3 KTTTSLDVITYGEAMAMFVAAETG-PLAGVGQFTKRVAGADLNVAIGLSRLGFKVGWMSR 61 Query: 67 VSDDQMGRFITGYLKDNKINTDQIRIDCTGAVTGLAFTEIKSPEDCSILMYRDNVADLNL 126 V +D G+++ L I+ + D ++ D +I +R A +L Sbjct: 62 VGNDSFGQYVRDTLTKEGIDQGCVTTDERYPTGFQLKSKNDDGSDPAIEYFRKGSAASHL 121 Query: 127 DPTEVSEDYIKQSKALLISGTALAKSPS-REAVFLALEYARKHDVVVFFDVDYRPYTWQS 185 + + DY+ Q++ L ++G A A S S RE F R + FD + RP W S Sbjct: 122 SLADYAADYVLQARHLHLTGVAPAISASSRELAFHLAREMRAAGKTISFDPNLRPTLWPS 181 Query: 186 EAETAVYYNLAAEKSDVIIGTREEFDMMEKLLNYEQSNDQVTAERWFSHYAKIVVIKHGG 245 A N A +D ++ E ++ L Y Q +D A+ + A+ V+IK G Sbjct: 182 RAAMVEGLNALAALADWVLPGIGEGEI---LTGYTQPDD--IAKFYLEQGARGVIIKLGA 236 Query: 246 DGSIAYTRDGQSHRGGIFKTKVLKTFGAGDSYASAFIYGLIQGLEIPQAMRLGGASASIV 305 G+ T D + G KV+ T GAGD +A + L++G +PQA+ G ++ Sbjct: 237 QGAYFRTADDAAMIAGQPVAKVVDTVGAGDGFAVGVVSALLEGKSLPQAVARGNRIGALA 296 Query: 306 ISKHSCSDAMPTRAEISAFMETAE 329 I S+ +P+RAE+ A +E A+ Sbjct: 297 IQVIGDSEGLPSRAELDA-LEAAQ 319 Lambda K H 0.318 0.134 0.385 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: 206 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: 332 Length of database: 327 Length adjustment: 28 Effective length of query: 304 Effective length of database: 299 Effective search space: 90896 Effective search space used: 90896 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 (21.7 bits) S2: 49 (23.5 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