Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate WP_037452835.1 N825_RS14310 amino acid ABC transporter permease
Query= SwissProt::P0AER5 (224 letters) >NCBI__GCF_000576635.1:WP_037452835.1 Length = 303 Score = 132 bits (332), Expect = 7e-36 Identities = 80/223 (35%), Positives = 131/223 (58%), Gaps = 6/223 (2%) Query: 6 WSSIVPSL--PYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVF 63 WS+I L P +++G+ +TL TV A+VI I+ G ++A+MRLSS ++ FA Y+ F Sbjct: 55 WSAIGEYLFDPTIIEGIKLTLLFTVLAMVISIVAGVVIAMMRLSSNPVLSGFASVYIWFF 114 Query: 64 RSIPL-VMVLLWF--YLIVPGFLQNVLGLSPKNDIRLISA-MVAFSMFEAAYYSEIIRAG 119 R PL V ++ WF L +P + L I +A ++A S+ E AY +EI+R G Sbjct: 115 RGTPLLVQIIFWFNIQLFIPSIDIGPIHLETNTLISAFTAALLALSLNETAYMAEIVRGG 174 Query: 120 IQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLAD 179 + ++ +GQS AA ALG T +Q++ ++LPQA R ++P + Q I + + TSLV V++ D Sbjct: 175 LLAVDKGQSEAATALGYTPFQTLTRVVLPQALRVIIPPVGNQTISMLKTTSLVSVVAAQD 234 Query: 180 FFRTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222 I ++ +E++L A Y V++ ASL+ +++RR Sbjct: 235 LLTRVQNIYAKNFLIIELLLVASIWYLVMTTVASLVQGWIERR 277 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: 180 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: 303 Length adjustment: 24 Effective length of query: 200 Effective length of database: 279 Effective search space: 55800 Effective search space used: 55800 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: 47 (22.7 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