Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease
Query= SwissProt::P0AER5 (224 letters) >NCBI__GCF_900115975.1:WP_092487756.1 Length = 234 Score = 145 bits (366), Expect = 6e-40 Identities = 85/226 (37%), Positives = 133/226 (58%), Gaps = 12/226 (5%) Query: 9 IVPSLPYLL-DGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIP 67 ++ +LP L+ G ITL+IT+ +V IG L G + + RLS + + A AYV+ FR P Sbjct: 4 VIENLPVLIFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTP 63 Query: 68 LVMVLLWFYLIVP-------GFLQNVLGLSPKNDI----RLISAMVAFSMFEAAYYSEII 116 L++ + Y +P F+ + G++P D R ++A++A S+ AY +EI Sbjct: 64 LLVQIFIVYFGIPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIF 123 Query: 117 RAGIQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLS 176 RAG+QSI RGQ AA +LGMTH Q+M+ +ILPQAF+ ++P L + I + +DTSL+ V+ Sbjct: 124 RAGVQSIERGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIG 183 Query: 177 LADFFRTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222 A+ R I R + L GF+Y +++ + S +V YL+RR Sbjct: 184 FAELTRNGQLIIARTYESFAIWLTVGFIYLIMTFTLSRIVDYLERR 229 Lambda K H 0.330 0.140 0.412 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: 139 Number of extensions: 7 Number of successful extensions: 2 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: 224 Length of database: 234 Length adjustment: 23 Effective length of query: 201 Effective length of database: 211 Effective search space: 42411 Effective search space used: 42411 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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