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 GFF2464 PS417_12565 2-dehydro-3-deoxygluconokinase
Query= SwissProt::P50845 (324 letters) >FitnessBrowser__WCS417:GFF2464 Length = 313 Score = 327 bits (837), Expect = 3e-94 Identities = 167/307 (54%), Positives = 219/307 (71%), Gaps = 3/307 (0%) Query: 2 KLDAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGNDQ 61 ++D ++FGE+MAMF A + G L V+ F K +AGA+SNVA GL+RLGF++ W+S+VGND Sbjct: 3 EIDILSFGETMAMFVAEQTGDLAHVAQFHKRIAGADSNVAIGLSRLGFKVAWLSRVGNDS 62 Query: 62 LGTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEGD-PQVTYYRKNSAASTLTTAE 120 LG F++ L +EG+D R + +PTG LKS+ + GD PQV Y+RK SAAS L+ A Sbjct: 63 LGRFVVDTLTQEGLDC-RHVAVDPAHPTGFQLKSREETGDDPQVEYFRKGSAASHLSIAA 121 Query: 121 YPRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATM 180 Q A HLH TGIPPALS ++ + +M MR AG+++SFDPN+RPSLW +Q TM Sbjct: 122 ISPALLQ-ARHLHATGIPPALSEATRELSVELMTQMRKAGRSVSFDPNLRPSLWANQQTM 180 Query: 181 VHTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGT 240 + IN LAGLADW PG+ EG LTG P IA +YL +GA VAIKLG +GAY++T Sbjct: 181 IREINALAGLADWVLPGLGEGRQLTGFDDPADIAAFYLDQGAEAVAIKLGPDGAYYRTHL 240 Query: 241 SEGFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDG 300 +GF+ RVD+VVDTVGAGDGFAVG+IS +L+ LS+ +AVQRGN IG+ VQ+ GDM+G Sbjct: 241 DQGFVAAVRVDKVVDTVGAGDGFAVGMISALLENLSFPEAVQRGNWIGSRAVQSRGDMEG 300 Query: 301 LPTREKL 307 LP R +L Sbjct: 301 LPARSEL 307 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: 346 Number of extensions: 17 Number of successful extensions: 4 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: 313 Length adjustment: 27 Effective length of query: 297 Effective length of database: 286 Effective search space: 84942 Effective search space used: 84942 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