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 AZOBR_RS22795 AZOBR_RS22795 spermidine/putrescine ABC transporter ATPase
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__azobra:AZOBR_RS22795 Length = 358 Score = 185 bits (469), Expect = 2e-51 Identities = 104/245 (42%), Positives = 145/245 (59%), Gaps = 8/245 (3%) Query: 34 ILKKTGATVGVYDTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVA 93 I + GA+ V + EI GE+ ++G SG GK+TLLR+L T G++ I D+ V Sbjct: 6 ITHRFGASTAVDNVTLEIKAGELVALLGPSGCGKTTLLRILAGFQAQTLGRVVIGDRVV- 64 Query: 94 TLNKEDLLQVRRKSMSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNAN 153 D L + + +VFQN+ LFPH T+ +N YGLE + ++ R R E L Sbjct: 65 -----DSLPPAGRGVGIVFQNYALFPHMTVAQNVAYGLEARGAARDAVRARVEAMLGLVK 119 Query: 154 LLDFKDQYPKQLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAK 213 L +D++PKQLSGG QQRV LARALA P ILL+DE F+ALD +R +MQ E+ +LQ + Sbjct: 120 LDAMRDRFPKQLSGGQQQRVALARALAIQPSILLLDEPFAALDKNLRLDMQIEIKQLQRR 179 Query: 214 FQKTIIFVSHDLNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTFVEDVD--RA 271 F T I V+HD EAL + DRIA++ GK+ Q GT E++ P +V FV + R Sbjct: 180 FGITTIMVTHDQEEALSMADRIAVLSRGKLEQFGTPEDVYDRPGTLFVNGFVGSANQLRG 239 Query: 272 KVITA 276 +V+ A Sbjct: 240 RVVRA 244 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: 290 Number of extensions: 7 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: 358 Length adjustment: 30 Effective length of query: 377 Effective length of database: 328 Effective search space: 123656 Effective search space used: 123656 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