Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate BWI76_RS14855 BWI76_RS14855 periplasmic binding protein/LacI transcriptional regulator
Query= uniprot:D8IZC6 (316 letters) >FitnessBrowser__Koxy:BWI76_RS14855 Length = 317 Score = 226 bits (575), Expect = 7e-64 Identities = 118/315 (37%), Positives = 191/315 (60%), Gaps = 8/315 (2%) Query: 3 KNTIAIACSTLL-----LAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHK 57 K +AIA + ++ LA AA A K + +G+ V D++NPFF A+ + A+ A K Sbjct: 6 KAWLAIAVAAVITTMTGLAPAASAAPQESKKIARIGLMVQDMSNPFFSAMERNAKQAAAK 65 Query: 58 INPDAKVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVA 117 I A + V ++ DL Q QI+ FI KVDLI+++A D G+ PA+++A+ AGI+V+A Sbjct: 66 IG--ATLNVQDAQVDLANQNTQIDAFIQQKVDLIIISAVDESGIEPAIQRAKAAGIIVIA 123 Query: 118 VDVAAAGADVTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFK 177 VD A GAD +M++ AG SC++L ++ GKG V++V+G P+ ++DR+ GCK + Sbjct: 124 VDTPAKGADAAIMTNAIQAGETSCEYLFSQMGGKGKVLLVDGTPIQTIIDRIKGCKNVAQ 183 Query: 178 KSPGIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSD 237 K P IKI+ Q + R G+ +++L A P + +F +NDP+A+GA LA+ QA ++ Sbjct: 184 KYPDIKIVG-QQASRNDRASGLMVTTDMLTANPDVSGIFGMNDPSALGAVLAVEQAGKAG 242 Query: 238 IKWISGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLP 297 ++GVDG+P+A LK S F + Q+P M +++++ +++G+ + L+P Sbjct: 243 AINVTGVDGSPEAVEELKRGGSPFIGTATQNPGEMVRQAISLAQDMVDGKPIASRTVLIP 302 Query: 298 VKLITRDNVADYQGW 312 L+TRDNV Y GW Sbjct: 303 SVLVTRDNVGSYPGW 317 Lambda K H 0.314 0.129 0.360 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: 255 Number of extensions: 9 Number of successful extensions: 2 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: 316 Length of database: 317 Length adjustment: 27 Effective length of query: 289 Effective length of database: 290 Effective search space: 83810 Effective search space used: 83810 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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