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 RR42_RS18590 RR42_RS18590 hypothetical protein
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__Cup4G11:RR42_RS18590 Length = 359 Score = 167 bits (423), Expect = 4e-46 Identities = 91/225 (40%), Positives = 135/225 (60%), Gaps = 4/225 (1%) Query: 16 TAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIYINEKRISDYDIHEL 75 T + V +DI DG+F V +GPSGCGK+T L+MI L +TTG I I + ++ E Sbjct: 16 TQVIRGVDIDIADGQFTVLVGPSGCGKSTLLRMIAGLEEITTGEIAIGNRVVNRLPPKER 75 Query: 76 RWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLDSVGLDPESYRHRKP 135 DI V Q AL+PHMT+ +N+A +L K KE+I ++ + +GLD S R P Sbjct: 76 --DIAMVFQNYALYPHMTVYDNMAFSLKLAKGDKEEIKRKVAKASAILGLD--SLLERYP 131 Query: 136 AELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDISALQKKIKKTIVFVT 195 +LSGG++QRV + RA+ DP + L DEP S LD R +++ +I L ++++ T V+VT Sbjct: 132 RQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKELHQRLRTTSVYVT 191 Query: 196 HDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLAS 240 HD EA+ + D+I VM+ G + Q P + +P+N FV F+ S Sbjct: 192 HDQIEAMTMADQIVVMRDGRVEQRGKPLALYDHPDNLFVAGFIGS 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: 270 Number of extensions: 15 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: 359 Length adjustment: 29 Effective length of query: 299 Effective length of database: 330 Effective search space: 98670 Effective search space used: 98670 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