Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate HSERO_RS07545 HSERO_RS07545 2-dehydro-3-deoxygluconokinase
Query= metacyc::MONOMER-12748 (320 letters) >FitnessBrowser__HerbieS:HSERO_RS07545 Length = 313 Score = 323 bits (828), Expect = 3e-93 Identities = 163/305 (53%), Positives = 214/305 (70%), Gaps = 1/305 (0%) Query: 4 IDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSL 63 +D++++GE +A+ VA+ G +V+ + +R+AGA++NVAIGLARLG KV W SRVGND+ Sbjct: 5 LDVVTWGEALALLVADEVGPFEEVEKYTRRLAGAETNVAIGLARLGLKVGWASRVGNDAF 64 Query: 64 GRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDLD 123 GRF+ + EG++ V D T QLK++ GG DP +EY+R+GSAASHL++ D D Sbjct: 65 GRFIRQRVAQEGVEVSRVITDMEFRTAIQLKAKAVGGADPAIEYYRKGSAASHLSVDDFD 124 Query: 124 PALL-RARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALMIR 182 ARHLHATGI PALS + + M R G ++SFDPNLRP LWPS+ +M + Sbjct: 125 AGYFGAARHLHATGIAPALSATTMAFAHQAMDFMRGQGKTISFDPNLRPMLWPSQEVMAQ 184 Query: 183 EINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQLDA 242 ++N LA A WVLPGL+EG++LTG DD +IA FYL++G + VVIKLGA GAY+R Sbjct: 185 QLNALAFKADWVLPGLSEGKILTGHDDAREIAGFYLERGVKLVVIKLGAEGAYWRNGQGE 244 Query: 243 GFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEGLP 302 G V GVPV +VVDTVGAGDGFAVG+IS +LE + +AV R N IG+ A+Q GDMEGLP Sbjct: 245 GRVAGVPVKEVVDTVGAGDGFAVGVISGMLEGLPVPQAVMRGNRIGAFAIQVVGDMEGLP 304 Query: 303 LRHEL 307 R EL Sbjct: 305 TRAEL 309 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: 358 Number of extensions: 16 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: 320 Length of database: 313 Length adjustment: 27 Effective length of query: 293 Effective length of database: 286 Effective search space: 83798 Effective search space used: 83798 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