Align deoxyribose kinase (EC 2.7.1.15) (characterized)
to candidate RR42_RS28860 RR42_RS28860 2-dehydro-3-deoxygluconokinase
Query= reanno::BFirm:BPHYT_RS25805 (328 letters) >FitnessBrowser__Cup4G11:RR42_RS28860 Length = 311 Score = 105 bits (261), Expect = 2e-27 Identities = 84/281 (29%), Positives = 121/281 (43%), Gaps = 20/281 (7%) Query: 42 FAMGPGGKGSNQAVAAARVGADVVFCTRIGNDAFGSIARATWAAEGITARASVIDGVSTG 101 + G GG SN +AAAR GA + + +G D FG A W E + R ID + Sbjct: 25 YLQGFGGDTSNFCIAAARQGARAGYISAVGEDTFGERLLALWTQERVDTRHVRIDAGAPT 84 Query: 102 AAHIFVDDNTGMNAIIVASGAAGTMEAADVDAIEADIAAARVFVTQLEQPLA-----AAR 156 + D G + SG+A + + + A A + V+ + ++ A Sbjct: 85 GVYFVTHDAHGHRFDYLRSGSAASHYSHENLPHHAIAEARYLHVSGISLAISTSACDAGL 144 Query: 157 RGLEVARKHGV---------ITVFNPAPAMPLDDAIFPLCDYITPNETEATALTGVPIAN 207 +E ARK G + ++ A A + F L D P+ + T LTG+ Sbjct: 145 AAMEHARKAGCQVTLDTNLRLRLWTLARARGIMREAFALTDVCLPSWDDITVLTGL---- 200 Query: 208 ADDARRAADVLLAKGVGTAIITLGEGGALLHSANQSLLVPAYHCGRVVETAGAGDGFTGG 267 DD D LL G+G + LGE GA + + LVP Y R V+ GAGD F G Sbjct: 201 -DDRDAIVDYLLGCGIGLVALKLGEEGAYVATPEARTLVPPYTV-RPVDATGAGDCFGGS 258 Query: 268 FAAALARGDDAITALRFGCALAGISVTRPGTAPSMPTLDEV 308 F A LA GDD A R+ A +S T G +P+++ V Sbjct: 259 FVARLAAGDDPFDAARYANVAAALSTTGYGAVAPIPSIETV 299 Lambda K H 0.318 0.133 0.384 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: 203 Number of extensions: 10 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: 328 Length of database: 311 Length adjustment: 28 Effective length of query: 300 Effective length of database: 283 Effective search space: 84900 Effective search space used: 84900 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: 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