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 Pf1N1B4_2538 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2538 Length = 374 Score = 190 bits (483), Expect = 4e-53 Identities = 100/245 (40%), Positives = 148/245 (60%), Gaps = 5/245 (2%) Query: 1 MIRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTI 60 ++ F V K Y D + V ++ LDI+ GEF +GPSG GKTT+L M+ T G I Sbjct: 14 LVSFRGVQKSY-DGENLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEI 72 Query: 61 YINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELL 120 + + I++ H+ DIG V Q ALFPHMT+ EN+A ++ +K + DR+ +L Sbjct: 73 QLAGRSINNVPPHKR--DIGMVFQNYALFPHMTVAENLAFPLTVRGLNKNDVSDRVKRVL 130 Query: 121 DSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDI 180 V LD ++ R PA+LSGG+QQRV + RAL +P ++LMDEP ALD R+ +Q +I Sbjct: 131 SMVQLD--TFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEI 188 Query: 181 SALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLAS 240 L +++ T+V+VTHD EAL + DR+ V GEI Q+A P+ + + P+N FV +F+ Sbjct: 189 KHLHQRLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAPPRSLYEEPKNTFVANFIGE 248 Query: 241 GHAFN 245 + N Sbjct: 249 NNRLN 253 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: 306 Number of extensions: 12 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: 374 Length adjustment: 29 Effective length of query: 299 Effective length of database: 345 Effective search space: 103155 Effective search space used: 103155 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