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_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 172 bits (435), Expect = 1e-47 Identities = 98/239 (41%), Positives = 139/239 (58%), Gaps = 5/239 (2%) Query: 2 IRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIY 61 +R D + K Y + V + +I DGE V +GPSGCGKTT L+MI L ++ GT+ Sbjct: 4 VRLDKLRKVYPNGHVG-VAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGGTLS 62 Query: 62 INEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLD 121 I E+ ++D I DI V Q AL+PHMT+ EN+ +L+ K +I R+ E Sbjct: 63 IGERVVND--IAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAAR 120 Query: 122 SVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDIS 181 + L E +PA LSGG++QRV + RAL DP + L+DEP S LD R ++ +I+ Sbjct: 121 MLEL--EQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIA 178 Query: 182 ALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLAS 240 + +++K T+V+VTHD EA+ LG RI V+ GG I Q+ TP + P N FV FL S Sbjct: 179 RIHQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGS 237 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: 268 Number of extensions: 18 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: 364 Length adjustment: 29 Effective length of query: 299 Effective length of database: 335 Effective search space: 100165 Effective search space used: 100165 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