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 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 179 bits (454), Expect = 1e-49 Identities = 98/245 (40%), Positives = 145/245 (59%), Gaps = 6/245 (2%) Query: 1 MIRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTI 60 +I +VSK + D A+++VTL++K GEF +GPSGCGKTT L++I + G I Sbjct: 9 IIEVSHVSKFFGDK--TALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEI 66 Query: 61 YINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELL 120 I+ K I+ H+ + V Q+ ALFPH+ + +NIA +LKK K+ I ++ L Sbjct: 67 RISGKEITQTPPHKR--PVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAAL 124 Query: 121 DSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDI 180 VG+ Y +R LSGG+QQRV + RA+ +P ++L+DEP +ALD R+ +Q ++ Sbjct: 125 KMVGMT--DYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMEL 182 Query: 181 SALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLAS 240 + K + T V+VTHD +EAL L D I VM G+I Q+ TP +I P N FV DF+ Sbjct: 183 KEMHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGE 242 Query: 241 GHAFN 245 + N Sbjct: 243 SNILN 247 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: 387 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: 463 Length adjustment: 30 Effective length of query: 298 Effective length of database: 433 Effective search space: 129034 Effective search space used: 129034 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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