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 Ga0059261_3653 Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__Korea:Ga0059261_3653 Length = 276 Score = 119 bits (297), Expect = 1e-31 Identities = 81/232 (34%), Positives = 127/232 (54%), Gaps = 14/232 (6%) Query: 18 AVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTT-----GTIYINEKRISD--Y 70 A+ +V++D+ FIGPSGCGK+T L+ +NR+ G I ++ + I D Sbjct: 43 AIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMNDTVASARVEGEITLDGENIYDKSM 102 Query: 71 DIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIH-DRITEL-LDSVGL--D 126 D+ +LR +G V Q+ FP +I EN+A P + ++ K D+I E L GL + Sbjct: 103 DVVQLRARVGMVFQKPNPFPK-SIYENVAYGPRIHGLARAKGDMDQIVERSLKRAGLWEE 161 Query: 127 PESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDISALQKK 186 + + LSGG+QQR+ + RA+A DP +ILMDEP SALDPI+ ++++ I L+ + Sbjct: 162 VKDRLNDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIATAKIEELIHELRGR 221 Query: 187 IKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFL 238 IV VTH+MQ+A + R G +V+ +I P + KD++ Sbjct: 222 Y--AIVIVTHNMQQAARVSQRTAFFHLGTLVEYGETDQIFTAPRQERTKDYI 271 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: 205 Number of extensions: 13 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: 276 Length adjustment: 27 Effective length of query: 301 Effective length of database: 249 Effective search space: 74949 Effective search space used: 74949 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 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