Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_109969948.1 DK846_RS15740 amino acid ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >NCBI__GCF_003173355.1:WP_109969948.1 Length = 250 Score = 207 bits (527), Expect = 2e-58 Identities = 107/239 (44%), Positives = 166/239 (69%), Gaps = 2/239 (0%) Query: 1 MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60 +++++++ K +G+ VLK ++ +VK+GE + IGPSG+GKST +RC+N L SG+V++ Sbjct: 7 ILKVEDIRKSFGSSEVLKGVSFNVKKGETICFIGPSGTGKSTLLRCINQLTIPDSGKVLL 66 Query: 61 NNLVLNHK-NKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119 N + H ++I R+ MVFQ+F L+ H+T ++N+ +A +K++ + K+A A K Sbjct: 67 NGEEVTHSGSQINHFRQKIGMVFQNFFLFDHLTAVRNVEIALLKVKGMNAKDARAKAMKE 126 Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179 L+ VG+ + A+ +PA LSGGQ QRV+IAR+L +LFDEPTSALDPE +EVL+VMK Sbjct: 127 LQQVGMAEWADHFPAELSGGQAQRVSIARALAMDPDVMLFDEPTSALDPELTREVLEVMK 186 Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGK 238 +++ TM+VVTHEMGFA VA++I+FME G I E+ P ++PK ER + F+G+ Sbjct: 187 KLA-LDGMTMLVVTHEMGFACSVANQILFMEHGVIKEQGSPQVLLNDPKFERCKAFIGQ 244 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: 149 Number of extensions: 8 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: 250 Length adjustment: 24 Effective length of query: 218 Effective length of database: 226 Effective search space: 49268 Effective search space used: 49268 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 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