Align Ribokinase; RK; EC 2.7.1.15 (characterized)
to candidate HSERO_RS08715 HSERO_RS08715 2-dehydro-3-deoxygluconokinase
Query= SwissProt::A0A0H2WZY4 (304 letters) >FitnessBrowser__HerbieS:HSERO_RS08715 Length = 308 Score = 108 bits (271), Expect = 1e-28 Identities = 84/279 (30%), Positives = 136/279 (48%), Gaps = 20/279 (7%) Query: 40 GGKGANQAIATARMQADTTFITKIGTDGVADFILEDFKVAHIDTSYIIKTAEAKTGQAFI 99 GG +N AIA AR A + +++ +G D +L ++ +D ++ TG F+ Sbjct: 30 GGDTSNFAIAAARQGAASAYLSAVGDDHFGQDLLALWQREEVDVRHVAIAPGGSTGIYFV 89 Query: 100 TVNAEGQNTIYVYGGANMTM-----TPEDVINAKDAIINADFVVAQLEVPIPAIISAFEI 154 T +A G + Y G+ + P + I A A+ + +A E A ++A Sbjct: 90 THDAAGHHFHYRRAGSAASAYQAKALPLEAIAAAGALHLSGISLAISESACEAGLAAMAH 149 Query: 155 AKAHGVTTVLNP---------APAKALPNELLSLIDIIVPNETEAELLSGIKVTNEQSMK 205 A+A GVTT L+ A+A E L DI +P+ + LL+G++ + ++ Sbjct: 150 ARASGVTTSLDTNLRLRLWPLERARARMEEAFRLCDICLPSWEDVSLLTGLE--DRDAIV 207 Query: 206 DNANYFLSIGIKTVLITLGKQGTYFATKNQSQHIEAYKVNAIDTTAAGDTFIGAFVSRLN 265 D LS G+K V LGK+G Y AT +Q + + Y V+++D T AGD F GAF++ L Sbjct: 208 DR---LLSYGVKLVAFKLGKEGCYVATSDQRRMVAPYPVDSLDATGAGDCFGGAFMAELM 264 Query: 266 KSQDNLADAIDFGNKASSLTVQKHGAQASIPLLEEVNQV 304 +D A A + N A++L+ +GA IP +V V Sbjct: 265 AGRDAFA-AARYANVAAALSTTGYGAVEPIPRRAQVEAV 302 Lambda K H 0.314 0.130 0.352 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: 191 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: 304 Length of database: 308 Length adjustment: 27 Effective length of query: 277 Effective length of database: 281 Effective search space: 77837 Effective search space used: 77837 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: 42 (22.0 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