Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate H281DRAFT_00856 H281DRAFT_00856 2-keto-3-deoxygluconate kinase
Query= reanno::Cup4G11:RR42_RS28860 (311 letters) >FitnessBrowser__Burk376:H281DRAFT_00856 Length = 311 Score = 400 bits (1027), Expect = e-116 Identities = 200/301 (66%), Positives = 235/301 (78%), Gaps = 3/301 (0%) Query: 4 DILAFGEALVEFNQQPDDPSRYLQGFGGDTSNFCIAAARQGARAGYISAVGEDTFGERLL 63 +ILA GEA++EFNQ D YLQGFGGDTSNFCIAAARQGAR G++SAVG D FG L+ Sbjct: 10 EILALGEAMIEFNQSAKDEPNYLQGFGGDTSNFCIAAARQGARTGFVSAVGADHFGRLLI 69 Query: 64 ALWTQERVDTRHVRIDAGAPTGVYFVTHDAHGHRFDYLRSGSAASHYSHENLPHHAIAEA 123 LW +E+VDT VR+D A TGVYFV+H GH FDYLR+GSAAS Y+ +LP AIA A Sbjct: 70 DLWEREQVDTALVRVDPHASTGVYFVSHGPDGHAFDYLRAGSAASRYAPRDLPLDAIAAA 129 Query: 124 RYLHVSGISLAISTSACDAGLAAMEHARKAGCQVTLDTNLRLRLWTLARARGIMREAFAL 183 + +H+SGISLAIS SACDA L A+ HAR G QV+ DTNLRL+LW L RAR +M EA Sbjct: 130 KVIHLSGISLAISLSACDAALEAITHARANGVQVSFDTNLRLKLWPLNRARAVMLEAIRQ 189 Query: 184 TDVCLPSWDDITVLTGLDDRDAIVDYLLGCGIGLVALKLGEEGAYVATPEARTLVPPYTV 243 TD+CLPSWDD+T LTGL RD IVD+LL G +VALKLG+EG+Y+ATP+ R +VP + V Sbjct: 190 TDICLPSWDDVTELTGLTGRDEIVDFLLSHGPRVVALKLGKEGSYIATPDERRVVPGHVV 249 Query: 244 RPVDATGAGDCFGGSFVARLAAGDDPFDAARYANVAAALSTTGYGAVAPIPS---IETVL 300 VDATGAGDCFGG+F+ARL GDDPF+AARYANVAAALST GYGAVAPIPS +E +L Sbjct: 250 NAVDATGAGDCFGGAFIARLVEGDDPFEAARYANVAAALSTQGYGAVAPIPSRAAVERIL 309 Query: 301 A 301 A Sbjct: 310 A 310 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: 356 Number of extensions: 6 Number of successful extensions: 1 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: 311 Length adjustment: 27 Effective length of query: 284 Effective length of database: 284 Effective search space: 80656 Effective search space used: 80656 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