Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate GFF195 PGA1_c01990 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__Phaeo:GFF195 Length = 410 Score = 413 bits (1062), Expect = e-120 Identities = 221/426 (51%), Positives = 290/426 (68%), Gaps = 16/426 (3%) Query: 1 MALASDPPKAGFRLSMLIYDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNF 60 M+ +DPPKA F+LSML+ DTR+RS+T Q + L+ + +L NN NL A G + ++ Sbjct: 1 MSTLTDPPKAQFQLSMLVNDTRYRSLTFQAIAALVLALAIWYLGNNLIQNLRAAGLNISY 60 Query: 61 SFLWTRAGYDLAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQ 120 FL +GYD+ Q LI Y + +H RA + G+LNTLLV+VL CI ATI G + GVLRLS Sbjct: 61 GFLGDPSGYDINQRLIEYDSQSSHARAAVVGVLNTLLVAVLACITATIFGVVAGVLRLSN 120 Query: 121 NWLVARIMTVYVETFRNIPLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWF 180 NWLV+++M VYVE FRNIP+L+WI+++ TI+ P P++FR G+ +SM Sbjct: 121 NWLVSKLMAVYVEIFRNIPVLIWIIIIFTIMTAVMPGPREFR--------GDNATSSM-L 171 Query: 181 FDSVAVTNRGTNLPAPAFDHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKA 240 FD A TNRG +P P F+ G+ +LN L ++A + SF RR A A Sbjct: 172 FDLFAFTNRGVYIPMPWFES-------GFFASGALNWLVVIAALVGSFLVMRRIEANATK 224 Query: 241 VQEATGTRPTTWWPSLLILFAPISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIA 300 QE TG RP T +L + P++ +L+ +G + P++ F+F GG ++ AL A Sbjct: 225 TQEKTGVRPKTKLIALGVWLVPLALVLFVMGLSWEVPELKGFNFKGGIKIGGPLIALWFA 284 Query: 301 LTLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFL 360 L++YT AFIAE VRAGIQAI++GQTEAA ALGLRPGR M+LV+LPQALRVI+PPLIS FL Sbjct: 285 LSIYTGAFIAENVRAGIQAINKGQTEAAAALGLRPGRIMNLVVLPQALRVIIPPLISNFL 344 Query: 361 NLTKNSSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKS 420 N+TKNSSLAIAV Y D+ TLGGITLNQTGR +EC+LL+ML YLT SL IS +MN+YN S Sbjct: 345 NITKNSSLAIAVGYADITATLGGITLNQTGRAIECVLLLMLFYLTASLLISMVMNVYNAS 404 Query: 421 IKLKER 426 +KLKER Sbjct: 405 VKLKER 410 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: 433 Number of extensions: 16 Number of successful extensions: 4 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: 426 Length of database: 410 Length adjustment: 32 Effective length of query: 394 Effective length of database: 378 Effective search space: 148932 Effective search space used: 148932 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: 50 (23.9 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