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 Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q9CES4 (247 letters) >FitnessBrowser__Cola:Echvi_1582 Length = 225 Score = 140 bits (353), Expect = 2e-38 Identities = 82/206 (39%), Positives = 124/206 (60%), Gaps = 9/206 (4%) Query: 21 VLKGITTKFEKGDVVCIIGPSGSGKSTFLRALNGLETATSGDIIIDGFNLT--DKNTNLN 78 VL+ I + GD + I+GPSGSGK+T L GL++A+SG + ++G L ++ Sbjct: 22 VLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDSASSGSVALNGHRLEGLSEDQRAA 81 Query: 79 LVRQNVGMVFQHFNLFPNMTVMQNITYAPVELKKMSKDDADKKAIQLLETVGLLDKKDAM 138 + Q +G +FQ+F L P +T ++N+ P+ELKK + DA +KA +LL+ VGL D+ Sbjct: 82 VRSQEIGFIFQNFQLLPTLTALENVM-VPLELKK--RKDAKQKATELLQQVGLGDRMTHY 138 Query: 139 PEMLSGGQKQRVAIARALAMNPDVMLFDEPTSALDPEMVGDVL--AVMQKLAEEGMTMLI 196 P LSGG++QRV+IARA A P ++ DEPT LD E G+++ + G T+++ Sbjct: 139 PTQLSGGEQQRVSIARAFANEPKILFADEPTGNLDTE-TGELIETLIFDLNKALGTTLIL 197 Query: 197 VTHEMGFARKVANRVIFTDGGVILED 222 VTH+ A K NR+I GG I E+ Sbjct: 198 VTHDTDLAAK-TNRIIHIKGGKIQEE 222 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: 127 Number of extensions: 10 Number of successful extensions: 3 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: 225 Length adjustment: 23 Effective length of query: 224 Effective length of database: 202 Effective search space: 45248 Effective search space used: 45248 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 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