Align 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized)
to candidate BPHYT_RS11300 BPHYT_RS11300 2-dehydro-3-deoxygluconokinase
Query= SwissProt::P50845 (324 letters) >FitnessBrowser__BFirm:BPHYT_RS11300 Length = 327 Score = 333 bits (854), Expect = 3e-96 Identities = 168/313 (53%), Positives = 219/313 (69%), Gaps = 2/313 (0%) Query: 3 LDAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGNDQL 62 LD +T+GE+MAMF A E G L V F+K +AGA+ NVA GL+RLGF++GWMS+VGND Sbjct: 8 LDVITYGEAMAMFVAAETGPLAGVGQFTKRVAGADLNVAIGLSRLGFKVGWMSRVGNDSF 67 Query: 63 GTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEG-DPQVTYYRKNSAASTLTTAEY 121 G ++ L KEG+D + + + PTG LKSK +G DP + Y+RK SAAS L+ A+Y Sbjct: 68 GQYVRDTLTKEGIDQG-CVTTDERYPTGFQLKSKNDDGSDPAIEYFRKGSAASHLSLADY 126 Query: 122 PRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATMV 181 DY A HLH+TG+ PA+SA ++ +H+ +MR AGKTISFDPN+RP+LWP +A MV Sbjct: 127 AADYVLQARHLHLTGVAPAISASSRELAFHLAREMRAAGKTISFDPNLRPTLWPSRAAMV 186 Query: 182 HTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGTS 241 +N LA LADW PGI EGE+LTG P+ IA +YL++GA V IKLG +GAYF+T Sbjct: 187 EGLNALAALADWVLPGIGEGEILTGYTQPDDIAKFYLEQGARGVIIKLGAQGAYFRTADD 246 Query: 242 EGFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDGL 301 + G V +VVDTVGAGDGFAVGV+S +L+G S AV RGN IGAL +Q GD +GL Sbjct: 247 AAMIAGQPVAKVVDTVGAGDGFAVGVVSALLEGKSLPQAVARGNRIGALAIQVIGDSEGL 306 Query: 302 PTREKLASFLSAQ 314 P+R +L + +AQ Sbjct: 307 PSRAELDALEAAQ 319 Lambda K H 0.317 0.135 0.399 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: 340 Number of extensions: 7 Number of successful extensions: 3 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: 324 Length of database: 327 Length adjustment: 28 Effective length of query: 296 Effective length of database: 299 Effective search space: 88504 Effective search space used: 88504 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