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 208681 DVU3161 ABC transporter, ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >MicrobesOnline__882:208681 Length = 349 Score = 174 bits (440), Expect = 4e-48 Identities = 95/239 (39%), Positives = 147/239 (61%), Gaps = 6/239 (2%) Query: 2 IRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIY 61 I D VS+ + D + AV++V+ +++ G+ V +GPSGCGK+TTL++I L +T+G I Sbjct: 4 IVLDKVSRHWGDVR--AVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSGRIL 61 Query: 62 INEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLD 121 I + +++ + + + V Q ALFPH+T+ +NI ++K + R+ ++ Sbjct: 62 IGGRDVTN--LPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRLDRAVE 119 Query: 122 SVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDIS 181 +GL RKP ELSGG+QQRV + RAL A+ + LMDEP S LD RQ ++++I Sbjct: 120 ILGLG--KLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIR 177 Query: 182 ALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLAS 240 ALQ+ + T+V+VTHD EA+++ DRI +MQGG IVQ ATP E+ P F F+ + Sbjct: 178 ALQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGT 236 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: 241 Number of extensions: 9 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: 349 Length adjustment: 28 Effective length of query: 300 Effective length of database: 321 Effective search space: 96300 Effective search space used: 96300 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