Align Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized)
to candidate WP_078212710.1 BXU11_RS12070 phosphate ABC transporter ATP-binding protein
Query= TCDB::Q9CES4 (247 letters) >NCBI__GCF_002017945.1:WP_078212710.1 Length = 252 Score = 149 bits (376), Expect = 5e-41 Identities = 83/248 (33%), Positives = 142/248 (57%), Gaps = 11/248 (4%) Query: 4 NTQIEVTDLHKSFGKNEVLKGITTKFEKGDVVCIIGPSGSGKSTFLRALNGLE-----TA 58 + +I+VTDL +G+ + L ++ + + V +IGPSG GKSTFLR +N + Sbjct: 3 DVKIDVTDLSLFYGEKKALSSVSMQIQANKVTALIGPSGCGKSTFLRCINRMNDLIPGVK 62 Query: 59 TSGDIIIDGFNLTDKNTNLNLVRQNVGMVFQHFNLFPNMTVMQNITYAP----VELKKMS 114 SG ++++G ++ DK ++ +R+ +GMVFQ N FP ++ +N+ Y P ++ K Sbjct: 63 ISGRMLVEGIDIYDKEVDVVNIRKKIGMVFQKSNPFPK-SIFENVAYGPRINGIKNKTQL 121 Query: 115 KDDADKKAIQLLETVGLLDKKDAMPEMLSGGQKQRVAIARALAMNPDVMLFDEPTSALDP 174 + + Q L D+ D LSGGQ+QR+ IAR LA+NPD++L DEP SALDP Sbjct: 122 DEIVEVSLRQAAIWEELKDRLDDSAMGLSGGQQQRLCIARTLAVNPDIILMDEPASALDP 181 Query: 175 EMVGDVLAVMQKLAEEGMTMLIVTHEMGFARKVANRVIFTDGGVILEDGTPEELFDSPKH 234 + ++ +L E+ T++IVTH M A + ++ F G ++E G +++F P+ Sbjct: 182 LSTSKIEELVHELKEQ-YTIVIVTHNMQQAARTSDHTAFFYMGELIEMGKTKDIFTKPEK 240 Query: 235 PRLQDFLS 242 + +D+++ Sbjct: 241 KQTEDYIT 248 Lambda K H 0.318 0.136 0.378 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: 145 Number of extensions: 8 Number of successful extensions: 4 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: 247 Length of database: 252 Length adjustment: 24 Effective length of query: 223 Effective length of database: 228 Effective search space: 50844 Effective search space used: 50844 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 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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