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_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= TCDB::Q9CES4 (247 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 156 bits (395), Expect = 5e-43 Identities = 91/240 (37%), Positives = 146/240 (60%), Gaps = 7/240 (2%) Query: 11 DLHKSFGKNEVLKGIT-TKFE--KGDVVCIIGPSGSGKSTFLRALNGLETATSGDIIIDG 67 D F K E G+ FE KG++ I+G SGSGKST +R LN L TSG ++IDG Sbjct: 32 DKEAIFEKTETTVGVQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDG 91 Query: 68 FNLTDKNTN--LNLVRQNVGMVFQHFNLFPNMTVMQNITYAPVELKKMSKDDADKKAIQL 125 ++ N + + + R + MVFQ F L P+MTV+QN + +E+ + K +++A+Q Sbjct: 92 EDIVAMNDDQLVKVRRAKLSMVFQSFALMPHMTVLQNAAFG-LEMDGVDKQTREQRALQA 150 Query: 126 LETVGLLDKKDAMPEMLSGGQKQRVAIARALAMNPDVMLFDEPTSALDPEMVGDVLAVMQ 185 LE VGL ++MP+ LSGG +QRV +AR LA++PD++L DE SALDP + ++ + Sbjct: 151 LEQVGLEAWAESMPDELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELL 210 Query: 186 KL-AEEGMTMLIVTHEMGFARKVANRVIFTDGGVILEDGTPEELFDSPKHPRLQDFLSKV 244 KL A+ T++ ++H++ A ++ +R+ +GG +++ GTPEE+ +P ++ F V Sbjct: 211 KLQAKAKRTIVFISHDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRGV 270 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: 268 Number of extensions: 19 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: 415 Length adjustment: 28 Effective length of query: 219 Effective length of database: 387 Effective search space: 84753 Effective search space used: 84753 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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