Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate WP_109939664.1 DLD82_RS03180 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_16275 (244 letters) >NCBI__GCF_003173335.1:WP_109939664.1 Length = 230 Score = 148 bits (373), Expect = 1e-40 Identities = 97/225 (43%), Positives = 130/225 (57%), Gaps = 11/225 (4%) Query: 1 MISIKNVNKWY----GDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKG 56 +I+ +V K Y GD L EV +GE I + GPSGSGKSTL+ + L+ G Sbjct: 7 VIAFHDVTKIYPLDSGDVTALNHVDVEVVRGEFIAIMGPSGSGKSTLLNMMGCLDIPTSG 66 Query: 57 DVVVDGTSIADPKTD-LPKLRSRV-GMVFQHFELFPHLTITENLTIAQIKVLGRSKEEAT 114 DV + G +I D L +LR V G +FQ F L L EN+ I G + T Sbjct: 67 DVFISGQNIKTMNDDQLTELRRDVLGFIFQQFNLILLLDALENVQYPLILKTGETG--CT 124 Query: 115 KKGLQLLERVGLSAHA-HKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVN 173 K+ +++LE VGL+ H H PGQLSGGQQQRVAIARAL DP ++L DEPT LD + Sbjct: 125 KRCMEVLEAVGLAPHLWHHRPGQLSGGQQQRVAIARALVNDPEILLCDEPTGNLDTKTGM 184 Query: 174 EVLDVMVQLANE-GMTMMCVTHEMGFARKVADRVIFMDQGKIIED 217 ++D++ QL E G T++ VTH+ A + ADR I ++ GKI E+ Sbjct: 185 AIMDLLTQLCREQGKTIVMVTHDPRIA-EYADRTILIEDGKIKEE 228 Lambda K H 0.321 0.136 0.394 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: 149 Number of extensions: 7 Number of successful extensions: 5 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: 244 Length of database: 230 Length adjustment: 23 Effective length of query: 221 Effective length of database: 207 Effective search space: 45747 Effective search space used: 45747 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 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