Align BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized)
to candidate BPHYT_RS11445 BPHYT_RS11445 putrescine/spermidine ABC transporter ATP-binding protein
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__BFirm:BPHYT_RS11445 Length = 388 Score = 183 bits (465), Expect = 7e-51 Identities = 98/246 (39%), Positives = 150/246 (60%), Gaps = 6/246 (2%) Query: 33 EILKKTGATVGVYDTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDV 92 +++KK G TV V N + +GE+F ++G SG GKSTLLR++ L +SGKI ID +D+ Sbjct: 35 DVVKKFGETVAVKGVNLSVKKGELFALLGSSGCGKSTLLRMMAGLESVSSGKILIDGEDL 94 Query: 93 ATLNKEDLLQVRRKSMSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNA 152 A L R+ ++M+FQ++ LFPH T+ N +GL+ + VPK E + R + AL+ Sbjct: 95 AQLPPY------RRPVNMMFQSYALFPHMTVEGNVAFGLKQEGVPKAELKDRVQTALELV 148 Query: 153 NLLDFKDQYPKQLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQA 212 + F + P QLSGG QQRV LAR+L P++LL+DE SALD IR+ Q EL+ + Sbjct: 149 QMGRFAKRKPNQLSGGQQQRVALARSLVKRPKLLLLDEPMSALDKQIRQRTQIELVNILD 208 Query: 213 KFQKTIIFVSHDLNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTFVEDVDRAK 272 K T + V+HD EA+ + R+A+M +G+I+Q+GT E+ P + + F+ + + Sbjct: 209 KVGVTCMMVTHDQEEAMTMAGRLAVMSEGEIVQLGTPHEVYEYPNSRFSAEFIGSTNLFE 268 Query: 273 VITAEN 278 T E+ Sbjct: 269 GHTVED 274 Lambda K H 0.316 0.135 0.364 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: 325 Number of extensions: 14 Number of successful extensions: 2 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: 407 Length of database: 388 Length adjustment: 31 Effective length of query: 376 Effective length of database: 357 Effective search space: 134232 Effective search space used: 134232 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 (21.6 bits) S2: 50 (23.9 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