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 RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 169 bits (429), Expect = 7e-47 Identities = 88/247 (35%), Positives = 143/247 (57%), Gaps = 5/247 (2%) Query: 6 NVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIYINEK 65 NV K Y+ + V+ + ++I DGEF V +GPSGCGK+T L+M+ L ++ G ++I +K Sbjct: 8 NVQKTYAGN-VKVVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGGEVHIGDK 66 Query: 66 RISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLDSVGL 125 ++ + E DI V Q AL+PHM++ +N+A +++ K +I R+ + L Sbjct: 67 VVNHLEPAER--DIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAAGILEL 124 Query: 126 DPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDISALQK 185 P RKP LSGG++QRV + RA+ +P + L DEP S LD R +++ ++ L + Sbjct: 125 AP--LLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKELHR 182 Query: 186 KIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLASGHAFN 245 +++ T ++VTHD EA+ L DR+ V+ GG + Q+ TP E+ P + FV F+ S Sbjct: 183 RLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPPMNL 242 Query: 246 TPILEAN 252 P+ N Sbjct: 243 VPVTRTN 249 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: 291 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: 328 Length of database: 367 Length adjustment: 29 Effective length of query: 299 Effective length of database: 338 Effective search space: 101062 Effective search space used: 101062 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: 49 (23.5 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