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 H281DRAFT_03485 H281DRAFT_03485 osmoprotectant transport system ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__Burk376:H281DRAFT_03485 Length = 372 Score = 251 bits (640), Expect = 3e-71 Identities = 116/243 (47%), Positives = 170/243 (69%) Query: 1 MIRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTI 60 MI+ ++SK+Y V+ + +++ GE V +GPSGCGKTTTLKMINRLI ++G I Sbjct: 1 MIKLSSISKRYEGASAPVVDGIDMEVGAGEICVLLGPSGCGKTTTLKMINRLIQPSSGKI 60 Query: 61 YINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELL 120 +I+ + ++++ ELR IGYV+QQI LFP+MT+EENI++VP L W K + R EL+ Sbjct: 61 FIDGRDTDEFEVVELRRQIGYVIQQIGLFPNMTVEENISVVPRLLGWDKARAKRRAAELM 120 Query: 121 DSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDI 180 + V LDP +Y R P +LSGG+QQRVGV RALA DP ++LMDEPF A+DPI+R+ +Q + Sbjct: 121 EIVALDPSTYLSRYPKDLSGGQQQRVGVARALATDPPVMLMDEPFGAIDPINRELIQDEF 180 Query: 181 SALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLAS 240 +Q+++KKTI+FV+HD+ EA+ + DRI + +GG + Q TP I+ P + F+ F+ + Sbjct: 181 LRIQQQVKKTIMFVSHDIDEAVKMADRIAIFRGGRLEQFDTPDTILARPASPFIAGFVGA 240 Query: 241 GHA 243 A Sbjct: 241 DRA 243 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: 290 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 328 Length of database: 372 Length adjustment: 29 Effective length of query: 299 Effective length of database: 343 Effective search space: 102557 Effective search space used: 102557 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