Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_011654832.1 RL_RS30155 amino acid ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >NCBI__GCF_000009265.1:WP_011654832.1 Length = 254 Score = 264 bits (674), Expect = 1e-75 Identities = 136/242 (56%), Positives = 179/242 (73%), Gaps = 2/242 (0%) Query: 1 MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60 MI ++ V K+YG L++IN+SV+ GE++V+ GPSGSGKST IRC+N LE GE+ V Sbjct: 13 MITMERVEKWYGAFQALRDINISVRSGERIVLCGPSGSGKSTLIRCINHLETYERGEIRV 72 Query: 61 NNLVLNHKNK-IEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119 ++L ++ K I+ R+ MVFQ FNL+PH+TVLQN LAPMK S+ EAEE A Sbjct: 73 GGILLGNQAKTIDAIRREVGMVFQQFNLFPHLTVLQNCMLAPMKAVGVSRAEAEERARGL 132 Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179 L+ V +L++A+ YP LSGGQQQRVAIAR+LC + +LFDEPTSALDPE ++EVLD M Sbjct: 133 LERVKILEQADKYPVQLSGGQQQRVAIARALCMRPKVMLFDEPTSALDPEMVKEVLDTMI 192 Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGKI 239 ++ + TM+ VTHEMGFA++VADR+IFM GAIVEE P+EFF+NP+ ER R FLG+I Sbjct: 193 ALADE-GMTMICVTHEMGFARQVADRVIFMASGAIVEEAPPAEFFTNPQHERTRKFLGEI 251 Query: 240 LK 241 L+ Sbjct: 252 LR 253 Lambda K H 0.317 0.133 0.372 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: 165 Number of extensions: 3 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: 242 Length of database: 254 Length adjustment: 24 Effective length of query: 218 Effective length of database: 230 Effective search space: 50140 Effective search space used: 50140 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 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