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 GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit
Query= TCDB::Q93A35 (328 letters) >FitnessBrowser__Marino:GFF1380 Length = 362 Score = 171 bits (432), Expect = 3e-47 Identities = 108/297 (36%), Positives = 165/297 (55%), Gaps = 11/297 (3%) Query: 14 DKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIYINEKRISDYDIH 73 DK A++++ L I DG+ +GPSG GKTT L++I L G I + K ++D + Sbjct: 13 DKFQALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIRFSGKDVTDLHVR 72 Query: 74 ELRWDIGYVLQQIALFPHMTIEENIA----IVPELKKWSKEKIHDRITELLDSVGLDPES 129 + R +G+V Q ALF HMT+ EN+A ++P ++ K +I R+ +LL+ V L E Sbjct: 73 DRR--VGFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRVKDLLEMVQL--EH 128 Query: 130 YRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDISALQKKIKK 189 R PA+LSGG++QR+ + RA+A P I+L+DEPF ALD R+ L++ + +L ++ Sbjct: 129 LADRYPAQLSGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRRWLRSLHDELHF 188 Query: 190 TIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLASGHAFNTPIL 249 T VFVTHD +EAL L D++ VM G I QV TP E+ P++ FV +FL + + I Sbjct: 189 TSVFVTHDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLGQVNVLSGKIR 248 Query: 250 EANFTVNDLIEADLFYSYQTSDGTLGISSTEPVENLVRRIAEEQSIPVTDEAGNYIG 306 + D L + D L + E L + +++ +P EA N IG Sbjct: 249 DGVMRQGD-AWIRLPEGCENDDAQLYLRPHE--VRLTQSASDDAHLPFRIEAINLIG 302 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: 269 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: 362 Length adjustment: 29 Effective length of query: 299 Effective length of database: 333 Effective search space: 99567 Effective search space used: 99567 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