Align 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178) (characterized)
to candidate H281DRAFT_00856 H281DRAFT_00856 2-keto-3-deoxygluconate kinase
Query= BRENDA::Q97U29 (313 letters) >FitnessBrowser__Burk376:H281DRAFT_00856 Length = 311 Score = 140 bits (353), Expect = 4e-38 Identities = 94/310 (30%), Positives = 154/310 (49%), Gaps = 14/310 (4%) Query: 3 DVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFG 62 +++ALGE +I+FN ++ F G NFCIA R ++ VG D FG Sbjct: 10 EILALGEAMIEFNQSAKDEPNYLQGF----GGDTSNFCIAAARQGARTGFVSAVGADHFG 65 Query: 63 KNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDIN 122 + +I+ + +DT+ ++VD + TG+YF+ G P Y R GSA SR +P D+ Sbjct: 66 RLLIDLWEREQVDTALVRVDPHASTGVYFVSHG---PDGHAFDYLRAGSAASRYAPRDLP 122 Query: 123 ENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSR----SLDTNIRPKLWSSLEKAKE 178 + + ++++H +GI+LAIS +A +A ++A A++ S DTN+R KLW L +A+ Sbjct: 123 LDAIAAAKVIHLSGISLAISLSACDAALEAITHARANGVQVSFDTNLRLKLW-PLNRARA 181 Query: 179 TILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDN 238 +L +++ DI + DD L +T DE G +V+ KLG +G+ + Sbjct: 182 VMLEAIRQTDI--CLPSWDDVTELTGLTGRDEIVDFLLSHGPRVVALKLGKEGSYIATPD 239 Query: 239 VKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELT 298 + + V D TGAGD G F++ ++G D + + A+ L G Sbjct: 240 ERRVVPGHVVNAVDATGAGDCFGGAFIARLVEGDDPFEAARYANVAAALSTQGYGAVAPI 299 Query: 299 PTLEDAERFL 308 P+ ER L Sbjct: 300 PSRAAVERIL 309 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: 219 Number of extensions: 11 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