Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate HSERO_RS05105 HSERO_RS05105 ribokinase
Query= reanno::Cup4G11:RR42_RS28860 (311 letters) >FitnessBrowser__HerbieS:HSERO_RS05105 Length = 319 Score = 124 bits (312), Expect = 2e-33 Identities = 94/294 (31%), Positives = 140/294 (47%), Gaps = 22/294 (7%) Query: 25 YLQGFGGDTSNFCIAAARQGARAGYISAVGEDTFGERLLALWTQERVDTRHVRIDAGAPT 84 + G GG SN +AAAR GA +ISA+G+D FG+ L+LW +E + HVR+ GAPT Sbjct: 39 FAMGPGGKGSNQAVAAARVGAPVRFISAIGKDAFGDFALSLWRRETI-APHVRVIDGAPT 97 Query: 85 GVYFV-THDAHGHRFDYLRSGSAASHYSHENLPHHAIAEARYLHVSGISLAISTSACDAG 143 G F+ +DA G + G AAS S +++ E + + + + + +A Sbjct: 98 GAAFIYVNDASGDNAIIVVPG-AASQLSEQDVER----ERQAIEAAKVFVTQLEQPPEAA 152 Query: 144 LAAMEHARKAGCQVTLDTNLRLRLWTLARARGIMREAFALTDVCLPSWDDITVLTG---- 199 LA ++ AR AG + A A + + L D P+ + +LTG Sbjct: 153 LAGLQIARAAGTTTVFNP---------APALAFPAQVYGLCDFITPNEHEAALLTGIEIH 203 Query: 200 -LDDRDAIVDYLLGCGIGLVALKLGEEGAYVATPEARTLVPPYTV-RPVDATGAGDCFGG 257 +DD D LL G+G + LG +G+ + + +P V+ GAGD F G Sbjct: 204 HIDDARRAADVLLERGVGCALITLGAQGSLLHSRSQSLHLPALCAGTVVETAGAGDAFNG 263 Query: 258 SFVARLAAGDDPFDAARYANVAAALSTTGYGAVAPIPSIETVLARMAQSVSVIA 311 +F A LA G +AAR A AA+S T G +PS + LA + SV+A Sbjct: 264 AFAAGLAEGMSAEEAARLATAVAAISVTRPGTAPSMPSRQEALALLDTHASVLA 317 Lambda K H 0.321 0.136 0.409 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: 250 Number of extensions: 14 Number of successful extensions: 4 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: 311 Length of database: 319 Length adjustment: 27 Effective length of query: 284 Effective length of database: 292 Effective search space: 82928 Effective search space used: 82928 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 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