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_RS07325 BWI76_RS07325 aminoimidazole riboside kinase
Query= SwissProt::Q53W83 (309 letters) >FitnessBrowser__Koxy:BWI76_RS07325 Length = 307 Score = 120 bits (300), Expect = 5e-32 Identities = 107/309 (34%), Positives = 150/309 (48%), Gaps = 23/309 (7%) Query: 3 EVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELG 62 +V G+ +V L+P+ G RLL GGA NVAV +ARLG GF+GRVG+D G Sbjct: 4 KVWVLGDAVVDLLPESEG-----RLLRC-PGGAPANVAVGIARLGGISGFIGRVGDDPFG 57 Query: 63 AMVEERLRAEGVDLTHFR-RAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPD 121 + L+ E VD++H R T + + G+ + + SA LA D Sbjct: 58 RFMRHTLQQELVDVSHMRLDGEHRTSTVVVDLDDQGERTFTFMVRPSADLFLAKE--DLP 115 Query: 122 YLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEE-ARGFL 180 ++LH+ I + P +R+ + AME+ K G RVS D N R LW +E L Sbjct: 116 QFAANQWLHVCSIALSAEP-SRSTTFAAMEKIKLAGGRVSFDPNIRPDLWQDQELLHACL 174 Query: 181 ERALPGVDLLFLSEEEAELLFGRVEEA-----LRALSAPEVVL-KRGAKGAWAFVDGRRV 234 +RAL +++ LSEEE + G + A + A PE++L +G G A + Sbjct: 175 DRALRMANVVKLSEEELVFISGSDDLAQGIASITARYQPELLLVTQGKAGVLAAFQQQFT 234 Query: 235 EGSAFAVEAVDPVGAGDAFAAGYLAG-AVWGLP-----VEERLRLANLLGASVAASRGDH 288 SA V +VD GAGDAF AG LA A G+P +E L LA GA ++G Sbjct: 235 HFSAKPVVSVDTTGAGDAFVAGLLASLAAKGMPTDIEGLEPTLTLAQTCGALATTAKGAM 294 Query: 289 EGAPYREDL 297 PY+ DL Sbjct: 295 TALPYQRDL 303 Lambda K H 0.320 0.139 0.407 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: 230 Number of extensions: 17 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: 309 Length of database: 307 Length adjustment: 27 Effective length of query: 282 Effective length of database: 280 Effective search space: 78960 Effective search space used: 78960 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 (21.8 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