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 H281DRAFT_02450 H281DRAFT_02450 glycine betaine/proline transport system ATP-binding protein
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__Burk376:H281DRAFT_02450 Length = 393 Score = 330 bits (847), Expect = 3e-95 Identities = 184/392 (46%), Positives = 259/392 (66%), Gaps = 17/392 (4%) Query: 4 KVKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMGLS 63 KV +E L K+FG K AL M+ G K E+ +TG VGV++ +FE+ EGEIFV+MGLS Sbjct: 5 KVVVEGLCKVFGTNPKQALAMLAGGATKEEVFARTGQIVGVHNVSFEVKEGEIFVLMGLS 64 Query: 64 GSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPHRTI 123 GSGKSTL+RL+NRL+EP++GK+ ID +DVA++ + +L +RRK MSMVFQ+F L P RT+ Sbjct: 65 GSGKSTLIRLINRLVEPSAGKVLIDGRDVASVPRAELTALRRKDMSMVFQSFALMPQRTV 124 Query: 124 LENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALANDP 183 L N +GLEV V ++ER RA L+ L F + P QLSGGMQQRVGLARALA +P Sbjct: 125 LSNAAFGLEVAGVSRKEREARAMTVLEQVGLAPFAAKLPAQLSGGMQQRVGLARALAVNP 184 Query: 184 EILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKDGKI 243 +++MDEAFSALDPL R+EMQ+ LL+LQ + Q+TI+FVSHDL EA+RIG RIAIM+ GK+ Sbjct: 185 SLMIMDEAFSALDPLKRKEMQNVLLDLQREQQRTILFVSHDLEEAMRIGTRIAIMEGGKV 244 Query: 244 MQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIM----IPALTTNI-DVDGPSVALK 298 +QIGT +EI+TNPA+DYV+ F E +D ++ +TA ++M +P + ++ +D SVA Sbjct: 245 VQIGTPQEIITNPADDYVRAFFEGIDTSRYLTAGDLMQTDAVPLMHSHSPQIDASSVAAT 304 Query: 299 KMKTEEVSSLMAVDRKRQFRG-VVTSEQAIAARKNNQSLKDVMTTDVGTVTKEMLVRDIL 357 + + + +D +R+ RG V E A+ K N V + + + D++ Sbjct: 305 LNGSADYA--FVLDSERKIRGFVCRDETGSASAKLNY---------VECIRRTTPLDDVV 353 Query: 358 PIIYDAPTPLAVVDDQGYLKGILIRGIVLEAL 389 + + PL VV+ G G + + VL L Sbjct: 354 ERVVASRAPLPVVEADGSYCGSVNKTNVLHVL 385 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: 391 Number of extensions: 14 Number of successful extensions: 1 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: 393 Length adjustment: 31 Effective length of query: 376 Effective length of database: 362 Effective search space: 136112 Effective search space used: 136112 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