Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate RR42_RS02585 RR42_RS02585 amino acid ABC transporter permease
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__Cup4G11:RR42_RS02585 Length = 227 Score = 102 bits (255), Expect = 9e-27 Identities = 75/216 (34%), Positives = 114/216 (52%), Gaps = 9/216 (4%) Query: 207 LGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPS-LLILFAPISA 265 LG + VSL + + AV+ WG M R +V + W+ + +F I Sbjct: 18 LGEGMLVSLK-ITVTAVVVGIVWGTILAMMRLSSV------KLLNWFAQGYVTIFRSIPL 70 Query: 266 LLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQT 325 ++ L F L PQ+ + F T+ LIA L+ AA+ +EI+RAGIQ++SRGQ Sbjct: 71 VMVLLWFFLIIPQLLQKAFNLSQASDLRMTSALIAFALFEAAYYSEIIRAGIQSVSRGQM 130 Query: 326 EAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGIT 385 AA A+G+ G++M LVILPQA R +VP L++Q + L +++SL + D G GI Sbjct: 131 FAAQAMGMTYGQSMRLVILPQAFRNMVPLLLTQGIILFQDTSLVYVSALADFFGQAYGIG 190 Query: 386 LNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSI 421 + GR +E +L L+Y I + S L+ Y K + Sbjct: 191 -ERDGRIVEMLLFAGLVYFIICFSASLLVKRYQKKV 225 Score = 43.1 bits (100), Expect = 8e-09 Identities = 30/96 (31%), Positives = 52/96 (54%), Gaps = 2/96 (2%) Query: 71 LAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTV 130 +A T S + T L EG+L +L ++V ++ + GTI+ ++RLS L+ Sbjct: 1 MAYTFDFSSINATTLDVLGEGMLVSLKITVTAVVVGIVWGTILAMMRLSSVKLLNWFAQG 60 Query: 131 YVETFRNIPLLLWILLMGTILAETRPVPKDFRLTEA 166 YV FR+IPL++ +L I+ + + K F L++A Sbjct: 61 YVTIFRSIPLVMVLLWFFLIIPQL--LQKAFNLSQA 94 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: 10 Number of successful extensions: 5 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: 227 Length adjustment: 27 Effective length of query: 399 Effective length of database: 200 Effective search space: 79800 Effective search space used: 79800 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