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_00987 H281DRAFT_00987 glycine betaine/proline transport system ATP-binding protein
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__Burk376:H281DRAFT_00987 Length = 429 Score = 311 bits (796), Expect = 3e-89 Identities = 171/388 (44%), Positives = 247/388 (63%), Gaps = 5/388 (1%) Query: 7 IEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMGLSGSG 66 +++L+KIFG R + A ++ QG +NEI ++TG V V D + + GEIFV+MGLSGSG Sbjct: 40 VKNLSKIFGPRPERAAELIRQGLGRNEIFEQTGNMVAVNDVSLSVKAGEIFVVMGLSGSG 99 Query: 67 KSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPHRTILEN 126 KSTL+RLLNRLIEPTSG++ ++ +D+A ++ +L VRRK M+MVFQ+F L P+RT+L+N Sbjct: 100 KSTLVRLLNRLIEPTSGQVILEGRDIAPMSTPELRDVRRKKMAMVFQSFALLPNRTVLDN 159 Query: 127 TEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALANDPEIL 186 YGLEV + K ER A AL L ++ P +LSGGMQQRVGLARALA +P +L Sbjct: 160 IAYGLEVAGLKKAERYDIARAALTRVGLGSYEKLLPGELSGGMQQRVGLARALAVNPSVL 219 Query: 187 LMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKDGKIMQI 246 LMDEAFSALDPLIR EMQ ELL LQ + Q+TI+F+SHD+ EA++IG RI IMKDG ++Q+ Sbjct: 220 LMDEAFSALDPLIRFEMQSELLRLQKEEQRTIVFISHDIEEAIKIGGRIGIMKDGCLIQV 279 Query: 247 GTGEEILTNPANDYVKTFVEDVDRAKVITAENIM--IPALTTNIDVDGPSVA-LKKMKTE 303 GT E++ +PA+DYV+ F +VD ++ + A ++M + + DV PS L ++ Sbjct: 280 GTPAELIQSPADDYVRDFFRNVDVSRFLKASSLMTRVERELISCDVAAPSERYLNQLIDS 339 Query: 304 EVSSLMAVDRKRQFRGVVTSEQAIAARKNNQSLKDVMTTDVGTVTKEMLVRDILPIIYDA 363 D +++G VT A + S+++ DV V + + + I + Sbjct: 340 GADCGYVCDEAGRYQGCVT--PASLRKTGAHSIREAFVNDVNAVPLDADLHQLATIALNQ 397 Query: 364 PTPLAVVDDQGYLKGILIRGIVLEALAD 391 + V D G L GI+ +L+ + + Sbjct: 398 QHDVPVTDTAGRLAGIVSCRAILKQVME 425 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: 428 Number of extensions: 8 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: 429 Length adjustment: 32 Effective length of query: 375 Effective length of database: 397 Effective search space: 148875 Effective search space used: 148875 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