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 PP_0868 PP_0868 ABC transporter ATP-binding subunit
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__Putida:PP_0868 Length = 385 Score = 249 bits (636), Expect = 8e-71 Identities = 130/315 (41%), Positives = 199/315 (63%), Gaps = 18/315 (5%) Query: 1 MIRFDNVSKKYSDD--KTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTG 58 MI N+SK ++ + AV++V+L + +GE VF+GPSGCGK+TTLKMINRLI T+G Sbjct: 1 MIELKNLSKTFNVNGKDVKAVDSVSLTVNEGEICVFLGPSGCGKSTTLKMINRLITPTSG 60 Query: 59 TIYINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITE 118 ++IN + + D LR IGYV+QQI LFP+MTIEENI +VP L W K+K H+R E Sbjct: 61 QVFINGEDTTGLDEVTLRRHIGYVIQQIGLFPNMTIEENITVVPRLLGWDKQKCHERARE 120 Query: 119 LLDSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQ 178 L+ + L+P+ Y R P ELSGG+QQR+GV+RALAAD ++LMDEPF A+DPI+R+ +Q Sbjct: 121 LMHMIKLEPKQYLQRYPRELSGGQQQRIGVIRALAADAPVLLMDEPFGAVDPINREMIQN 180 Query: 179 DISALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFL 238 + +Q+ + KT++ V+HD+ EA+ LGD+I + + G+++Q+ P ++ +P +DFV +F+ Sbjct: 181 EFFEMQRALNKTVIMVSHDIDEAIKLGDKIAIFRAGKLLQLDHPDTLLAHPADDFVSNFV 240 Query: 239 ASGHAFNTPILEANFTVNDLIEADLFYSYQTSDGTLGISSTEPVENLVRRIAE--EQSIP 296 + T+ L+ L + +D +S PV + + + E + + Sbjct: 241 GQ-----------DSTLKRLL---LVRAEDAADNAPSVSPETPVGDALELLDEHDRRYVV 286 Query: 297 VTDEAGNYIGTVSNK 311 VTD +G V + Sbjct: 287 VTDAQNKALGYVRRR 301 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: 320 Number of extensions: 6 Number of successful extensions: 1 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: 385 Length adjustment: 29 Effective length of query: 299 Effective length of database: 356 Effective search space: 106444 Effective search space used: 106444 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