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 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__PV4:5208462 Length = 378 Score = 180 bits (456), Expect = 7e-50 Identities = 105/275 (38%), Positives = 159/275 (57%), Gaps = 22/275 (8%) Query: 44 VYDTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQV 103 V D + IN GEIF ++G SGSGKSTLLR+L +PT G+I++D QD+ + + Sbjct: 36 VDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGRIYLDGQDITDMPPYE---- 91 Query: 104 RRKSMSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPK 163 + ++M+FQ++ LFPH T+ +N +GL+ +PK E +R ++ L ++ + + P Sbjct: 92 --RPINMMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRVKEMLKLVHMEPYAKRKPN 149 Query: 164 QLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSH 223 QLSGG +QRV LAR+LA P++LL+DE ALD +R +MQ E++++ T + V+H Sbjct: 150 QLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVDILEAVGVTCVMVTH 209 Query: 224 DLNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTF-----------VEDVDRAK 272 D EA+ + +RIAIM DG I Q G+ +I +PAN V F VED Sbjct: 210 DQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFIGSVNLFEGDIVEDEVDHV 269 Query: 273 VITAENIMIP-----ALTTNIDVDGPSVALKKMKT 302 VI NI P ++T++D VA++ KT Sbjct: 270 VINVANIPQPFYVGYGVSTSVDTTQVWVAIRPEKT 304 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: 317 Number of extensions: 16 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: 378 Length adjustment: 31 Effective length of query: 376 Effective length of database: 347 Effective search space: 130472 Effective search space used: 130472 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