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 CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 135 bits (339), Expect = 4e-36 Identities = 84/238 (35%), Positives = 138/238 (57%), Gaps = 6/238 (2%) Query: 36 KKTGATVGVYDTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATL 95 K T V NFE+ GE ++G SG GK+TL R + RLI+PTSG+I + +++ + Sbjct: 328 KTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRTILRLIQPTSGEIIFNGENITHI 387 Query: 96 NKEDLLQVRRKSMSMVFQN--FGLFPHRTILENTEYGLEVQNVPKE--ERRKRAEKALDN 151 K L ++R K + ++FQ+ L P +I ++ L+V + + ER+++ + LD Sbjct: 388 GKTALRKLR-KDIQIIFQDPYASLNPKLSIGQSILEPLQVHKLYRNDSERKQKVLELLDK 446 Query: 152 ANLLDFK-DQYPKQLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLEL 210 L + ++YP + SGG +QRV +ARALA P+ ++ DE+ SALD ++ ++ + + +L Sbjct: 447 VGLKEEHFNRYPHEFSGGQRQRVVIARALALQPKFIICDESVSALDVSVQAQVLNLIKDL 506 Query: 211 QAKFQKTIIFVSHDLNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTFVEDV 268 Q++F T IF+SHDL I DRI +M GKI + G E+I P Y + +E + Sbjct: 507 QSEFGLTYIFISHDLAVVKHISDRILVMNKGKIEEEGFPEQIFYAPKAAYTQKLIEAI 564 Score = 112 bits (281), Expect = 2e-29 Identities = 72/229 (31%), Positives = 122/229 (53%), Gaps = 10/229 (4%) Query: 44 VYDTNFEINEGEIFVIMGLSGSGKS----TLLRLLNRLIEPTSGKIFIDDQDVATLNKED 99 V +F++ +G + I+G SGSGKS +++RL + +G+I +D + L+ + Sbjct: 23 VKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGEIDFEDISLLNLSSNE 82 Query: 100 LLQVRRKSMSMVFQN--FGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDF 157 + Q+R +SM+FQ L P T + + + K+ AL N L Sbjct: 83 IRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHRKVDQAEAKKHTIALFNEVQLPR 142 Query: 158 KDQ----YPKQLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAK 213 ++ YP Q+SGG +QRV +A AL+ DP++L+ DE +ALD +++ + LL+L+ + Sbjct: 143 PEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQKTILQLLLKLKQE 202 Query: 214 FQKTIIFVSHDLNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVK 262 +IF+SHDL I D +A+M G+I++ G + I NP + Y K Sbjct: 203 RNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKSIFENPQHPYTK 251 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: 515 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 407 Length of database: 568 Length adjustment: 34 Effective length of query: 373 Effective length of database: 534 Effective search space: 199182 Effective search space used: 199182 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: 51 (24.3 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