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 Pf6N2E2_4681 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4681 Length = 392 Score = 277 bits (709), Expect = 3e-79 Identities = 145/280 (51%), Positives = 200/280 (71%), Gaps = 4/280 (1%) Query: 5 VKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMGLSG 64 ++ E + IF R K AL ++++G + EIL++TG VGV + I +GEI V+MGLSG Sbjct: 4 IRFEDVDVIFSNRPKAALDLLDKGLSRPEILQQTGLIVGVEKASLSIEKGEICVLMGLSG 63 Query: 65 SGKSTLLRLLNRLIEPTSGKIFIDDQ----DVATLNKEDLLQVRRKSMSMVFQNFGLFPH 120 SGKS+LLR +N L + GK+F++ + D+A+ + +L +R K ++MVFQ F L P Sbjct: 64 SGKSSLLRCINGLNTVSRGKLFVEHEGRQIDIASCSPAELKMMRTKRIAMVFQKFALMPW 123 Query: 121 RTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALA 180 T+ EN +GLE+Q P++ERRK ++ L+ L ++++ P +LSGGMQQRVGLARALA Sbjct: 124 LTVRENISFGLEMQGRPEKERRKLVDEKLELVGLTQWRNKKPDELSGGMQQRVGLARALA 183 Query: 181 NDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKD 240 D +ILLMDE FSALDPLIR+ +QDELLELQ K QKTI+FVSHDL+EAL++G RIAIMKD Sbjct: 184 MDADILLMDEPFSALDPLIRQGLQDELLELQRKLQKTIVFVSHDLDEALKLGTRIAIMKD 243 Query: 241 GKIMQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIM 280 GKI+Q EEI+ NPA+DYV+TFV + V+ ++M Sbjct: 244 GKIIQYSKPEEIVLNPADDYVRTFVAHTNPLNVLCGRSLM 283 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: 372 Number of extensions: 10 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: 392 Length adjustment: 31 Effective length of query: 376 Effective length of database: 361 Effective search space: 135736 Effective search space used: 135736 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