Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate WP_028310949.1 H566_RS0107445 amino acid ABC transporter permease
Query= SwissProt::P0AER5 (224 letters) >NCBI__GCF_000482785.1:WP_028310949.1 Length = 227 Score = 285 bits (728), Expect = 7e-82 Identities = 141/221 (63%), Positives = 175/221 (79%) Query: 2 YEFDWSSIVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVN 61 YE+DWSSI +LP L G+ ++L+IT AVV+GI WGT+LAV+RLS+ A + WFA YVN Sbjct: 3 YEYDWSSIPGALPLLASGMKVSLEITAVAVVVGIAWGTVLAVLRLSNSAALRWFATGYVN 62 Query: 62 VFRSIPLVMVLLWFYLIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQ 121 +FR+IPLVMVLLWF+LIVP L + L P DIRL+SA+V F++FE+AYY+EIIRAGIQ Sbjct: 63 LFRAIPLVMVLLWFFLIVPQLLGALFSLDPHTDIRLVSALVGFALFESAYYAEIIRAGIQ 122 Query: 122 SISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFF 181 S+ RGQ+ AA ALGMT WQ+M L++LPQAFR MVPLLLTQ IVLFQDTSLVYV +LADFF Sbjct: 123 SVPRGQTMAASALGMTRWQAMTLVVLPQAFRNMVPLLLTQAIVLFQDTSLVYVSALADFF 182 Query: 182 RTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222 TA +G+RDG VE++LFAG VYFV+ S +V +RR Sbjct: 183 GTAYKVGDRDGRIVELLLFAGAVYFVLCFGLSRIVQGYQRR 223 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: 203 Number of extensions: 3 Number of successful extensions: 1 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: 227 Length adjustment: 22 Effective length of query: 202 Effective length of database: 205 Effective search space: 41410 Effective search space used: 41410 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 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