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 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 152 bits (383), Expect = 1e-41 Identities = 93/243 (38%), Positives = 136/243 (55%), Gaps = 9/243 (3%) Query: 19 VNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIYINEKRISDYD--IHELR 76 + + L + GE +GPSGCGKTT L+ I L ++ G+I IN K +S + + Sbjct: 19 LRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSIAINGKTVSADGCFVAPEK 78 Query: 77 WDIGYVLQQIALFPHMTIEENIAI-VPELKKWSKEKIHDRITELLDSVGLDPESYRHRKP 135 IG + Q ALFPH+T+ +NI V +L K S+ R+ E+L V L E R P Sbjct: 79 RSIGMIFQDYALFPHLTVADNILFGVRQLDKQSRSV---RLEEMLSLVKL--EGLGKRYP 133 Query: 136 AELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDISALQKKIKKTIVFVT 195 ELSGG+QQRV + RALA +P ++L+DEPFS +D R+ L +I A+ K + VFVT Sbjct: 134 HELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEIRAILKARNVSAVFVT 193 Query: 196 HDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLASGHAFNTPILEANFTV 255 H EA A D + + + G IVQ P+ + ++P +V DFL + + + LEA + Sbjct: 194 HSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLGASNYLDVR-LEAGQLI 252 Query: 256 NDL 258 + L Sbjct: 253 STL 255 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: 227 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: 341 Length adjustment: 28 Effective length of query: 300 Effective length of database: 313 Effective search space: 93900 Effective search space used: 93900 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