Align BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized)
to candidate N515DRAFT_0067 N515DRAFT_0067 phosphate transport system ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__Dyella79:N515DRAFT_0067 Length = 268 Score = 126 bits (317), Expect = 5e-34 Identities = 79/231 (34%), Positives = 130/231 (56%), Gaps = 13/231 (5%) Query: 18 AVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPL-----TTGTIYINEKRISD--Y 70 A+ + +DI + + IGPSGCGK+T L++ NR+ + G I ++E+ I D Y Sbjct: 36 ALKGINMDIPEKKVTAIIGPSGCGKSTLLRIFNRIYAIYPKLEAKGEIMLDEENILDTRY 95 Query: 71 DIHELRWDIGYVLQQIALFPHMTIEENIAI-VPELKKWSKEKIHDRITELLDSVGL--DP 127 +++LR +G V Q+ FP MTI EN+A + ++ S+ + R+ + L S L + Sbjct: 96 SMNKLRSKVGMVFQKPVPFP-MTIFENVAYGIRHHERLSRADMEIRVEQALRSAALWDEV 154 Query: 128 ESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDISALQKKI 187 + + LSGG+QQR+ + R +A P ++L+DEP SALDPI+ R++Q + L K Sbjct: 155 KDKLKQNALGLSGGQQQRLCIARGIALKPEVLLLDEPTSALDPIATGRIEQLVEEL--KS 212 Query: 188 KKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFL 238 + TIV VTH+MQ+A D M GE+++ ++I P +D++ Sbjct: 213 EYTIVIVTHNMQQAARCSDLTAFMYLGELIEFDRTEQIFTKPGKKQTEDYI 263 Lambda K H 0.318 0.136 0.386 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: 194 Number of extensions: 6 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: 328 Length of database: 268 Length adjustment: 26 Effective length of query: 302 Effective length of database: 242 Effective search space: 73084 Effective search space used: 73084 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 (21.7 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