Align 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178) (characterized)
to candidate RR42_RS28860 RR42_RS28860 2-dehydro-3-deoxygluconokinase
Query= BRENDA::Q97U29 (313 letters) >FitnessBrowser__Cup4G11:RR42_RS28860 Length = 311 Score = 137 bits (346), Expect = 3e-37 Identities = 93/305 (30%), Positives = 146/305 (47%), Gaps = 14/305 (4%) Query: 2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEF 61 +D++A GE L++FN P R++ F G NFCIA R I+ VG D F Sbjct: 3 IDILAFGEALVEFNQQPDDPSRYLQGF----GGDTSNFCIAAARQGARAGYISAVGEDTF 58 Query: 62 GKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDI 121 G+ ++ + +DT H+++D + TG+YF+ Y R GSA S S E++ Sbjct: 59 GERLLALWTQERVDTRHVRIDAGAPTGVYFVTHD---AHGHRFDYLRSGSAASHYSHENL 115 Query: 122 NENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSR----SLDTNIRPKLWSSLEKAK 177 + + +R +H +GI+LAIS +A +A + A E A+ +LDTN+R +LW +L +A+ Sbjct: 116 PHHAIAEARYLHVSGISLAISTSACDAGLAAMEHARKAGCQVTLDTNLRLRLW-TLARAR 174 Query: 178 ETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKD 237 + D V + DD +L + D D G+ ++ KLG +GA Sbjct: 175 GIMREAFALTD--VCLPSWDDITVLTGLDDRDAIVDYLLGCGIGLVALKLGEEGAYVATP 232 Query: 238 NVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNEL 297 + Y V D TGAGD G+FV+ G D + + A+ L T G Sbjct: 233 EARTLVPPYTVRPVDATGAGDCFGGSFVARLAAGDDPFDAARYANVAAALSTTGYGAVAP 292 Query: 298 TPTLE 302 P++E Sbjct: 293 IPSIE 297 Lambda K H 0.317 0.136 0.383 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: 230 Number of extensions: 13 Number of successful extensions: 5 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: 313 Length of database: 311 Length adjustment: 27 Effective length of query: 286 Effective length of database: 284 Effective search space: 81224 Effective search space used: 81224 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 (21.6 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