Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate 14790 b0653 glutamate and aspartate transporter subunit (NCBI)
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__Keio:14790 Length = 224 Score = 92.0 bits (227), Expect = 2e-23 Identities = 62/199 (31%), Positives = 105/199 (52%), Gaps = 8/199 (4%) Query: 218 LAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSLLI-LFAPISALLYGLGFHLDY 276 + + AV+ WG AV + P W+ + +F I ++ L F+L Sbjct: 26 ITVTAVVIGILWG------TMLAVMRLSSFAPVAWFAKAYVNVFRSIPLVMVLLWFYLIV 79 Query: 277 PQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPG 336 P + + + ++A +++ AA+ +EI+RAGIQ+ISRGQ+ AA ALG+ Sbjct: 80 PGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSISRGQSSAALALGMTHW 139 Query: 337 RTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGITLNQTGRELECM 396 ++M L+ILPQA R +VP L++Q + L +++SL +S D T I + G ++E + Sbjct: 140 QSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTASTIG-ERDGTQVEMI 198 Query: 397 LLMMLIYLTISLTISSLMN 415 L +Y ISL+ S L++ Sbjct: 199 LFAGFVYFVISLSASLLVS 217 Score = 47.4 bits (111), Expect = 4e-10 Identities = 34/88 (38%), Positives = 48/88 (54%), Gaps = 6/88 (6%) Query: 88 LIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPL---LLWI 144 L++GL+ TL ++V ++ + GT++ V+RLS VA YV FR+IPL LLW Sbjct: 16 LLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIPLVMVLLWF 75 Query: 145 LLM--GTILAETRPVPK-DFRLTEAMKA 169 L+ G + PK D RL AM A Sbjct: 76 YLIVPGFLQNVLGLSPKNDIRLISAMVA 103 Lambda K H 0.326 0.139 0.419 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: 8 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 426 Length of database: 224 Length adjustment: 27 Effective length of query: 399 Effective length of database: 197 Effective search space: 78603 Effective search space used: 78603 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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