Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate BPHYT_RS09175 BPHYT_RS09175 2-dehydro-3-deoxygluconokinase
Query= reanno::Cup4G11:RR42_RS28860 (311 letters) >FitnessBrowser__BFirm:BPHYT_RS09175 Length = 312 Score = 399 bits (1026), Expect = e-116 Identities = 198/296 (66%), Positives = 233/296 (78%) Query: 4 DILAFGEALVEFNQQPDDPSRYLQGFGGDTSNFCIAAARQGARAGYISAVGEDTFGERLL 63 +ILA GEA++EFNQ D YLQGFGGDTSNFCIAAARQGA+ G++SAVG D FG L+ Sbjct: 11 EILALGEAMIEFNQSAKDQPNYLQGFGGDTSNFCIAAARQGAQTGFVSAVGADHFGRLLV 70 Query: 64 ALWTQERVDTRHVRIDAGAPTGVYFVTHDAHGHRFDYLRSGSAASHYSHENLPHHAIAEA 123 LW +E+VDT VR+D A TGVYFV+H +GH FDYLR+GSAAS Y+ +LP AIA A Sbjct: 71 DLWEREQVDTSLVRVDPQASTGVYFVSHGPNGHAFDYLRAGSAASRYAPHDLPLDAIAAA 130 Query: 124 RYLHVSGISLAISTSACDAGLAAMEHARKAGCQVTLDTNLRLRLWTLARARGIMREAFAL 183 + +H+SGISLAIS SACDA L A+ HAR G +V+ DTNLRL+LW LARAR +M EA Sbjct: 131 KVIHLSGISLAISLSACDAALEAIAHARANGVRVSFDTNLRLKLWPLARARAVMLEAIRQ 190 Query: 184 TDVCLPSWDDITVLTGLDDRDAIVDYLLGCGIGLVALKLGEEGAYVATPEARTLVPPYTV 243 TD+CLPSWDD+T LTGL RD IVD+LL G +VALKLG+EG+Y+ATP R +VP + V Sbjct: 191 TDICLPSWDDVTDLTGLTGRDEIVDFLLSHGPSVVALKLGKEGSYIATPNERRVVPGHVV 250 Query: 244 RPVDATGAGDCFGGSFVARLAAGDDPFDAARYANVAAALSTTGYGAVAPIPSIETV 299 VDATGAGDCFGG+F+AR+ AGDDPF AARYANVAAALST GYGAVAPIPS TV Sbjct: 251 NAVDATGAGDCFGGAFIARIVAGDDPFTAARYANVAAALSTQGYGAVAPIPSRATV 306 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: 9 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: 312 Length adjustment: 27 Effective length of query: 284 Effective length of database: 285 Effective search space: 80940 Effective search space used: 80940 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