Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate 6937298 Sama_1468 putative macrolide efflux ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::P0AAG3 (241 letters) >FitnessBrowser__SB2B:6937298 Length = 230 Score = 137 bits (345), Expect = 2e-37 Identities = 90/228 (39%), Positives = 131/228 (57%), Gaps = 13/228 (5%) Query: 1 MITLKNVSKWY----GHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQG 56 MI+L+ ++K + Q L +++ E V + GPSGSGKSTL+ + L+ G Sbjct: 1 MISLQALTKSFRMGDAEVQALRGVDIHIRQNEFVAIMGPSGSGKSTLMNIIGCLDRPTSG 60 Query: 57 EITVDGIVVNDKKTD-LAKLRSR-VGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPA- 113 ++G V D L+ +R+R +G VFQ F L P LS ++N+ L L+ + P Sbjct: 61 NYLLNGSAVGGLSDDALSAVRNREIGFVFQSFHLLPRLSALDNVLLP----LRFSETPRG 116 Query: 114 -REKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMI 172 R+ A++LLERVGL + P QLSGGQ+QRVAIARAL P +L DEPT ALD + Sbjct: 117 DRQHAIELLERVGLGQRLDHRPNQLSGGQRQRVAIARALVNRPTLLLADEPTGALDSKTS 176 Query: 173 NEVLDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPK 220 E++ + EL G T+++VTHE A + A R+I M +G + +D K Sbjct: 177 VEIMALFDELHLSGQTIVLVTHEEEVA-ECAGRIIRMRDGVVQQDKQK 223 Lambda K H 0.320 0.135 0.383 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: 116 Number of extensions: 6 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: 241 Length of database: 230 Length adjustment: 23 Effective length of query: 218 Effective length of database: 207 Effective search space: 45126 Effective search space used: 45126 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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