Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate SMc02119 SMc02119 general L-amino acid transport permease ABC transporter protein
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__Smeli:SMc02119 Length = 397 Score = 279 bits (713), Expect = 1e-79 Identities = 167/424 (39%), Positives = 246/424 (58%), Gaps = 34/424 (8%) Query: 5 SDPPKAGFRLSMLIYDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLW 64 ++ P+ +I D + R I Q + +++ A + W+++N NL + F+ Sbjct: 6 TNAPERSRSSGSIINDPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASGYDFVR 65 Query: 65 TRAGYDLAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLV 124 +RAG+D+ Q+LI +++D T+ RAL+ G +NTLLV++ G I ATI+G I+G+ RLS NW++ Sbjct: 66 SRAGFDVGQSLISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWII 125 Query: 125 ARIMTVYVETFRNIPLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSV 184 A++ YVE FRNIP LL I + + P +D A FD + Sbjct: 126 AKLSLAYVEVFRNIPPLLVIFFWYSGVLSILPQARD---------------ALALPFD-I 169 Query: 185 AVTNRGTNLPAPAFDHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEA 244 ++NRG P P + LA + ++AS + F A+ Q A Sbjct: 170 FLSNRGVAFPRPIAEEG-----------AEYTLLAFVIAVAASVF----FARYARKRQLA 214 Query: 245 TGTR-PTTWWPSLLILFAP-ISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALT 302 TG R P W LI+ P ++ L+ G D P KF+ TGG + F +L +AL+ Sbjct: 215 TGERLPVLWTVLGLIIGLPLVTFLVTGAPITFDIPVAGKFNLTGGSVVGPEFMSLFLALS 274 Query: 303 LYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNL 362 YTAAFIAEIVRAGI+ +S+GQTEAA+ALG+RP T LV++PQA+R+I+PPL SQ+LNL Sbjct: 275 FYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNL 334 Query: 363 TKNSSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIK 422 TKNSSLA+A+ Y DL +GG LNQTG+ +E + + +++YL++SL S MN YN + Sbjct: 335 TKNSSLAVAIGYADL-VAVGGTILNQTGQSIEIVSIWLIVYLSLSLATSLFMNWYNARMA 393 Query: 423 LKER 426 L ER Sbjct: 394 LVER 397 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: 402 Number of extensions: 20 Number of successful extensions: 3 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: 397 Length adjustment: 31 Effective length of query: 395 Effective length of database: 366 Effective search space: 144570 Effective search space used: 144570 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