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 AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__azobra:AZOBR_RS30410 Length = 371 Score = 187 bits (474), Expect = 5e-52 Identities = 99/241 (41%), Positives = 147/241 (60%), Gaps = 6/241 (2%) Query: 2 IRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIY 61 +R D V Y + + ++ LDIK GEFF F+GPSGCGKTT L++I G + Sbjct: 19 VRIDGVDLSYGSHRV--LKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVT 76 Query: 62 INEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLD 121 I + IS H+ D+G V Q AL+PHMT+ N+A E ++ + +I R+ LD Sbjct: 77 IGGRDISGLPAHKR--DVGMVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALD 134 Query: 122 SVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDIS 181 VGL + R+P++LSGG+QQRV + R + +P ++L+DEP S LD R +++Q++ Sbjct: 135 LVGL--KHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELL 192 Query: 182 ALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLASG 241 +LQ+K+ T +FVTHD +EA + DRI VM+ G + QV TPQE+ +P N FV FL + Sbjct: 193 SLQRKLGLTTIFVTHDQEEANTICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGTA 252 Query: 242 H 242 + Sbjct: 253 N 253 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: 283 Number of extensions: 14 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: 371 Length adjustment: 29 Effective length of query: 299 Effective length of database: 342 Effective search space: 102258 Effective search space used: 102258 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