Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate GFF2245 HP15_2195 amino acid ABC transporter, permease protein
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__Marino:GFF2245 Length = 395 Score = 287 bits (735), Expect = 3e-82 Identities = 177/410 (43%), Positives = 237/410 (57%), Gaps = 33/410 (8%) Query: 19 YDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPY 78 YD R RS+ Q V + L G L++N N+E++G F FL AG+ + L+PY Sbjct: 17 YDPRVRSLFFQAVAIALVFWGGWILVDNTLSNMESRGISTGFGFLGETAGFGIIMNLVPY 76 Query: 79 SNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNI 138 ++ R GL NTLLVS +G + ATILG IIGV RLS NWLVA++ VY+E RNI Sbjct: 77 DATMSYGRTFWVGLTNTLLVSAMGVVAATILGFIIGVARLSSNWLVAKMALVYIEVIRNI 136 Query: 139 PLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAF 198 PLLL I + P P+ +++ G ++ + NRG LP P Sbjct: 137 PLLLQIFFWYFAVLSNLPSPR-----QSVDVGG-----------ALFLNNRGLYLPDPVT 180 Query: 199 DHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTW--WPSL 256 G+V G LAI AV+ W AK Q ATG T+ ++ Sbjct: 181 QEGFGIVWGGI-------LLAIAAVVGIRIW--------AKKRQLATGQIFPTFKVGVAI 225 Query: 257 LILFAPISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAG 316 L+L IS L+ G D P + F+F GG ++ AL IAL+LYTA+FIAEIVR+G Sbjct: 226 LVLVPIISYLVAGRPLEWDLPALRGFNFGGGITIIPELAALWIALSLYTASFIAEIVRSG 285 Query: 317 IQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMD 376 I ++S+GQTEA+ ALGL G T+ LV++PQA+RVI+PPL SQ+LNL KNSSLA A+ Y D Sbjct: 286 ILSVSKGQTEASKALGLPNGLTLRLVVIPQAMRVIIPPLTSQYLNLVKNSSLATAIGYPD 345 Query: 377 LRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426 L G TLNQTG+ +E + + M +YLTISL IS MN+YN+++ +KER Sbjct: 346 LVAVFMGTTLNQTGQAVEVVAITMAVYLTISLLISLFMNIYNRAVAIKER 395 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: 435 Number of extensions: 23 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: 395 Length adjustment: 31 Effective length of query: 395 Effective length of database: 364 Effective search space: 143780 Effective search space used: 143780 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