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 BWI76_RS26750 BWI76_RS26750 PfkB domain-containing protein
Query= SwissProt::E0J5J4 (309 letters) >FitnessBrowser__Koxy:BWI76_RS26750 Length = 311 Score = 547 bits (1410), Expect = e-160 Identities = 272/308 (88%), Positives = 289/308 (93%) Query: 1 MSKKIAVIGECMIELSEKGADVKRGFGGDTLNTSVYIARQVDPAALTVHYVTALGTDSFS 60 MSKKIAVIGECMIELSEKGA V RGFGGDTLNTSVYIARQ D +AL VHYVTALGTD+FS Sbjct: 1 MSKKIAVIGECMIELSEKGAAVNRGFGGDTLNTSVYIARQTDASALGVHYVTALGTDTFS 60 Query: 61 QQMLDAWHGENVDTSLTQRMENRLPGLYYIETDSTGERTFYYWRNEAAAKFWLESEQSAA 120 QQML++W ENV T L QRM +RLPGLYYIETD TGERTFYYWRNEAAAKFWLESEQSAA Sbjct: 61 QQMLESWQSENVQTDLIQRMADRLPGLYYIETDDTGERTFYYWRNEAAAKFWLESEQSAA 120 Query: 121 ICEELANFDYLYLSGISLAILSPTSREKLLSLLRECRANGGKVIFDNNYRPRLWASKEET 180 ICEELA FDYLYLSGISLAIL+PTSREKLL+LLRECRANGGKVIFDNNYRPRLW+SKEET Sbjct: 121 ICEELATFDYLYLSGISLAILNPTSREKLLTLLRECRANGGKVIFDNNYRPRLWSSKEET 180 Query: 181 QQVYQQMLECTDIAFLTLDDEDALWGQQPVEDVIARTHNAGVKEVVVKRGADSCLVSIAG 240 QQVYQQML CTDIAFLTLDDEDALWG++PV +VIARTH AGV+EVVVKRGADSCLV+IAG Sbjct: 181 QQVYQQMLSCTDIAFLTLDDEDALWGEKPVAEVIARTHAAGVEEVVVKRGADSCLVAIAG 240 Query: 241 EGLVDVPAVKLPKEKVIDTTAAGDSFSAGYLAVRLTGGSAENAAKRGHLTASTVIQYRGA 300 + +DVPAVKLPKEKV+DTTAAGDSFSAGYLAVRLTGG AE+AAKRGHLTASTVIQYRGA Sbjct: 241 QPQLDVPAVKLPKEKVVDTTAAGDSFSAGYLAVRLTGGDAESAAKRGHLTASTVIQYRGA 300 Query: 301 IIPREAMP 308 IIPREAMP Sbjct: 301 IIPREAMP 308 Lambda K H 0.316 0.132 0.384 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: 441 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: 309 Length of database: 311 Length adjustment: 27 Effective length of query: 282 Effective length of database: 284 Effective search space: 80088 Effective search space used: 80088 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