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_691 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_691 Length = 351 Score = 181 bits (459), Expect = 2e-50 Identities = 101/240 (42%), Positives = 148/240 (61%), Gaps = 6/240 (2%) Query: 5 DNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIYINE 64 +NV K Y AV +V L + +G+ F+GPSGCGKTT L+MI L LT G I ++ Sbjct: 7 ENVEKHYGS--ACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLTGGEIRLDG 64 Query: 65 KRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLDSVG 124 + I H+ + G V Q +ALFPHMT+ ENIA +L+ SK R+ ELL+ + Sbjct: 65 EDIGHTPAHQRNF--GMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELLELIQ 122 Query: 125 LDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDISALQ 184 L + R A+LSGG++QRV + RA+A+ P I+L+DEP SALD R+ +Q +I LQ Sbjct: 123 L--QEMIDRPVAKLSGGQRQRVAIARAIASRPKILLLDEPLSALDAKLRESMQVEIRQLQ 180 Query: 185 KKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLASGHAF 244 +++ T + VTHD +EA+ + D + V+ + QV +P EI ++P N+FV DF+ SG+ F Sbjct: 181 QRLNITTIMVTHDQREAMTMADIVVVLGEHRVQQVGSPIEIYRHPANEFVADFIGSGNIF 240 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: 262 Number of extensions: 17 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: 351 Length adjustment: 28 Effective length of query: 300 Effective length of database: 323 Effective search space: 96900 Effective search space used: 96900 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