Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate 3608990 Dshi_2380 ABC transporter related (RefSeq)
Query= TCDB::P0AAG3 (241 letters) >FitnessBrowser__Dino:3608990 Length = 257 Score = 148 bits (373), Expect = 1e-40 Identities = 90/217 (41%), Positives = 134/217 (61%), Gaps = 5/217 (2%) Query: 1 MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60 MI L+ VSK +G +VL + KGE +V+ G SG+GKS ++K+V GL G+I V Sbjct: 10 MIELRGVSKAFGPKEVLRGVDLVIPKGESMVIIGGSGTGKSVMLKSVLGLISPDAGQILV 69 Query: 61 DGIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVK-VLKRDKAPAREKALK 119 DG V +K + +R GM+FQ LF L + +N++ ++ LKR +A AR+ A++ Sbjct: 70 DGKDV--EKVERDAFLARFGMLFQGGALFDSLPVWQNVSFRLLRGALKRPRAEARDIAIE 127 Query: 120 LLERVGLSAH-ANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDV 178 L RVGL+ A++FPA+LSGG Q+RV +ARA+ +P + FDEPT+ LDP M + D+ Sbjct: 128 KLRRVGLTPDVADQFPAELSGGMQKRVGLARAIAAEPEIIFFDEPTTGLDPIMSGVINDL 187 Query: 179 MVELANE-GMTMMVVTHEMGFARKVANRVIFMDEGKI 214 + E+ E G T M +TH+M R +A+ V + GKI Sbjct: 188 IREIVVEMGATAMTITHDMTSVRAIADDVAMLHGGKI 224 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: 167 Number of extensions: 14 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: 241 Length of database: 257 Length adjustment: 24 Effective length of query: 217 Effective length of database: 233 Effective search space: 50561 Effective search space used: 50561 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