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 AO353_25420 AO353_25420 spermidine/putrescine ABC transporter ATP-binding protein
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25420 Length = 372 Score = 186 bits (471), Expect = 1e-51 Identities = 105/238 (44%), Positives = 147/238 (61%), Gaps = 10/238 (4%) Query: 7 VSKKYSDDKTA--AVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIYINE 64 V K Y D + A+ ++ LDI+D EFF +GPSGCGKTT L+MI T G I + Sbjct: 17 VRKVYGDPHSGPVALKSIDLDIRDNEFFTLLGPSGCGKTTLLRMIAGFEFPTQGEILLYG 76 Query: 65 KRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIV----PELKKWSKEKIHDRITELL 120 + I+D ++ + V Q ALFPHMTI EN+A P K SK +I +R+ E+L Sbjct: 77 ENIADRPPYQR--PVNTVFQHYALFPHMTIAENLAFGLESHPMGKVLSKAQIAERVREML 134 Query: 121 DSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDI 180 V + E + R+P +LSGG+QQRV + RALA P ++L+DEP SALD RQ +++++ Sbjct: 135 ALVQM--ERFATRRPTQLSGGQQQRVALARALAPHPKVLLLDEPLSALDLKLRQAMREEL 192 Query: 181 SALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFL 238 A+Q K T +FVTHD +EAL + DRI V+ GE+ QV P++I + P N FV DF+ Sbjct: 193 KAIQAKTGITFIFVTHDQEEALTMSDRIAVLSEGEVQQVGRPEDIYERPRNRFVADFI 250 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: 265 Number of extensions: 6 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: 372 Length adjustment: 29 Effective length of query: 299 Effective length of database: 343 Effective search space: 102557 Effective search space used: 102557 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