Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate WP_012404721.1 BPHY_RS27410 amino acid ABC transporter permease
Query= SwissProt::P0AER5 (224 letters) >NCBI__GCF_000020045.1:WP_012404721.1 Length = 219 Score = 114 bits (284), Expect = 2e-30 Identities = 70/216 (32%), Positives = 121/216 (56%), Gaps = 8/216 (3%) Query: 9 IVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIPL 68 ++ +LP LL G ++TLK + + V+G+L G ++A+M +S +A A+AYV++ R PL Sbjct: 7 VINTLPVLLLGAMVTLKFALASAVLGLLVGFIVAIMGISGQPIIAGIARAYVSLMRGTPL 66 Query: 69 VMVLLWFYLIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSISRGQS 128 ++ + Y +P + L P + + ++A + AY SE +R I IS+GQ Sbjct: 67 LVQIFVVYYGLPDL---GISLDPTS-----AGILALTANAGAYLSESMRGAILGISQGQW 118 Query: 129 SAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTASTIG 188 AA +LG+TH Q+++ +I PQA R VP L I L +DTSLV V+++ + R A + Sbjct: 119 GAAHSLGLTHMQTLRYVICPQALRMAVPSLGNTLISLIKDTSLVSVITVTEMLRAAQEVI 178 Query: 189 ERDGTQVEMILFAGFVYFVISLSASLLVSYLKRRTA 224 + + L A +Y+++S S + +++ R A Sbjct: 179 ASTFQPLPLYLAAAAIYWLLSTGMSWVQRHVEVRLA 214 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: 134 Number of extensions: 4 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: 219 Length adjustment: 22 Effective length of query: 202 Effective length of database: 197 Effective search space: 39794 Effective search space used: 39794 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: 45 (21.9 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