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_5137 PP_5137 ferric iron ABC transporter, ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__Putida:PP_5137 Length = 352 Score = 180 bits (457), Expect = 4e-50 Identities = 101/241 (41%), Positives = 146/241 (60%), Gaps = 8/241 (3%) Query: 2 IRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIY 61 I+ N+ K++ A+N+V+LDI GE +GPSGCGKTT L+ I L GT+Y Sbjct: 10 IKVRNIHKRFG--AFTALNDVSLDIAAGELVCLLGPSGCGKTTLLRCIAGLERQDRGTLY 67 Query: 62 INEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLD 121 I E+ ISD + D G + Q ALFP++T+E NIA L +E+ R+ E+L+ Sbjct: 68 IGERDISD--LSPQARDYGILFQSYALFPNLTVEANIAY--GLTGSGREQARQRVAEMLE 123 Query: 122 SVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDIS 181 VGL ++ P +LSGG+QQRV + RALA P ++L+DEP SALD R+ L ++ Sbjct: 124 LVGLSGSEKKY--PGQLSGGQQQRVALARALAPSPSLLLLDEPMSALDARVREHLCTELR 181 Query: 182 ALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLASG 241 LQ+++ T + VTH+ EA+ + DRI VM G++ Q ATPQEI +P FV +F+ G Sbjct: 182 QLQRQLGITTLMVTHNQDEAMLMADRIAVMNNGQVEQYATPQEIYDHPATPFVAEFVGQG 241 Query: 242 H 242 + Sbjct: 242 N 242 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: 277 Number of extensions: 7 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: 352 Length adjustment: 28 Effective length of query: 300 Effective length of database: 324 Effective search space: 97200 Effective search space used: 97200 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