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 WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >NCBI__GCF_000526715.1:WP_024852149.1 Length = 263 Score = 139 bits (350), Expect = 8e-38 Identities = 81/213 (38%), Positives = 128/213 (60%), Gaps = 10/213 (4%) Query: 7 VSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIYINEKR 66 +S Y + N+ L+I G+ IG SGCGK+T L+MI L+ + G + IN K Sbjct: 13 LSHSYKKQLPPVLTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGVVRINGKT 72 Query: 67 ISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLDSVGLD 126 + +W++ + Q+ +L+P M++ EN A+ K+K DR+ ELLD VGL Sbjct: 73 VVK---PSAKWNM--MFQKPSLYPWMSVRENAALGLVFAGTYKQK-QDRVEELLDMVGLS 126 Query: 127 PESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDISALQKK 186 ++ + ELSGG+QQRV + R+LA +P I+L+DEPFSALD +R LQ +++ + + Sbjct: 127 --EHKDKNVQELSGGQQQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQICHE 184 Query: 187 IKKTIVFVTHDMQEALALGDRICVM--QGGEIV 217 T++ VTHD++EA+A+ D++ +M GEIV Sbjct: 185 QGITMIMVTHDIEEAIAMADKVVIMSHNPGEIV 217 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: 172 Number of extensions: 8 Number of successful extensions: 4 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: 263 Length adjustment: 26 Effective length of query: 302 Effective length of database: 237 Effective search space: 71574 Effective search space used: 71574 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 Apr 09 2024. 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