Align deoxyribose kinase (EC 2.7.1.15) (characterized)
to candidate PP_4934 PP_4934 heptose 7-phosphate kinase/heptose 1-phosphate adenylyltransferase
Query= reanno::Burk376:H281DRAFT_01116 (320 letters) >FitnessBrowser__Putida:PP_4934 Length = 473 Score = 58.5 bits (140), Expect = 3e-13 Identities = 45/142 (31%), Positives = 66/142 (46%), Gaps = 5/142 (3%) Query: 157 LEVARKHGVTTVFNPAPALPLDDDIFPLCDYITPNETEAAALTGVPIANVDDARRAADVL 216 ++ AR G+ + +P D I+ ITPN +E + G + + + +L Sbjct: 163 IQAARAKGIPVLADPKGK---DFSIYRGASLITPNLSEFETIVGRCVDEAELVAKGLQLL 219 Query: 217 LAKGVGTVIVTLGEGG-ALLHDATQSIWLPAFRCGAVVETAGAGDGFTGGFAAALARGED 275 +G ++VT GE G LL ++ LPA R V + GAGD AAA+A GED Sbjct: 220 QDLDLGALLVTRGEHGMTLLRVGQPALHLPA-RAREVFDVTGAGDTVISTLAAAIAAGED 278 Query: 276 AISAMRFGCALAGISVTRAGTA 297 A+ AGI V + GTA Sbjct: 279 LPHAVALANLAAGIVVGKLGTA 300 Lambda K H 0.318 0.132 0.377 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: 264 Number of extensions: 12 Number of successful extensions: 1 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: 473 Length adjustment: 30 Effective length of query: 290 Effective length of database: 443 Effective search space: 128470 Effective search space used: 128470 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: 50 (23.9 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