Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate BWI76_RS07325 BWI76_RS07325 aminoimidazole riboside kinase
Query= metacyc::MONOMER-12748 (320 letters) >FitnessBrowser__Koxy:BWI76_RS07325 Length = 307 Score = 112 bits (281), Expect = 9e-30 Identities = 92/280 (32%), Positives = 135/280 (48%), Gaps = 13/280 (4%) Query: 36 GADSNVAIGLARLGFKVAWLSRVGNDSLGRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKS 95 GA +NVA+G+ARLG ++ RVG+D GRF+ TL+ E +D +R D H T + Sbjct: 29 GAPANVAVGIARLGGISGFIGRVGDDPFGRFMRHTLQQELVDVSHMRLDGEHRTSTVVVD 88 Query: 96 REDGGDDPRVEYFRRGSAASHLAISDLDPALLRARHLHATGIPPALS-DSARELSGHLMH 154 +D G + + R SA LA DL P + LH I ALS + +R + M Sbjct: 89 LDDQG-ERTFTFMVRPSADLFLAKEDL-PQFAANQWLHVCSI--ALSAEPSRSTTFAAME 144 Query: 155 TQRSAGHSVSFDPNLRPALWPSEALMIREINRLAALAHWVLPGLAEGRLLTGRDDPAD-I 213 + AG VSFDPN+RP LW + L+ ++R +A+ V E ++G DD A I Sbjct: 145 KIKLAGGRVSFDPNIRPDLWQDQELLHACLDRALRMANVVKLSEEELVFISGSDDLAQGI 204 Query: 214 AAFYLDQGAEAVVIKLGAHGAYYRTQLDAGFVEGVPVAQVVDTVGAGDGFAVGLISAL-- 271 A+ E +++ G G Q PV VDT GAGD F GL+++L Sbjct: 205 ASITARYQPELLLVTQGKAGVLAAFQQQFTHFSAKPVVS-VDTTGAGDAFVAGLLASLAA 263 Query: 272 ----LESRGILEAVQRANWIGSRAVQSRGDMEGLPLRHEL 307 + G+ + A G+ A ++G M LP + +L Sbjct: 264 KGMPTDIEGLEPTLTLAQTCGALATTAKGAMTALPYQRDL 303 Lambda K H 0.321 0.138 0.414 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: 257 Number of extensions: 13 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: 320 Length of database: 307 Length adjustment: 27 Effective length of query: 293 Effective length of database: 280 Effective search space: 82040 Effective search space used: 82040 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