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_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >NCBI__GCF_000230695.2:WP_015448118.1 Length = 255 Score = 153 bits (387), Expect = 4e-42 Identities = 83/232 (35%), Positives = 136/232 (58%), Gaps = 3/232 (1%) Query: 9 KKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIYINEKRIS 68 K+Y + A+ V+L G IG SG GK+T L+++ L G + ++ + + Sbjct: 19 KRYG--RLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGRPLQ 76 Query: 69 DYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLDSVGLDPE 128 D+ LR +GYV+Q LFPH+T N+A++P W++E+I R +L L P Sbjct: 77 RSDVLPLRRRVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIRQRAEQLAALTHL-PT 135 Query: 129 SYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDISALQKKIK 188 R PAELSGG++QRV ++RAL ADP +L+DEP ALDP+ R LQ ++ + ++ Sbjct: 136 GVLERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDPVVRHELQDELKQIFDQLG 195 Query: 189 KTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLAS 240 KT++ VTHD+ EA +R+ +++ G ++Q T +++ + P + FV F+A+ Sbjct: 196 KTVIVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNRFVAA 247 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: 184 Number of extensions: 4 Number of successful extensions: 2 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: 255 Length adjustment: 26 Effective length of query: 302 Effective length of database: 229 Effective search space: 69158 Effective search space used: 69158 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 Sep 24 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