Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate Pf1N1B4_916 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_916 Length = 375 Score = 301 bits (770), Expect = 3e-86 Identities = 177/399 (44%), Positives = 246/399 (61%), Gaps = 34/399 (8%) Query: 31 VVLLLFLAGLVW-LLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYSNDDTHFRALI 89 ++ ++ + G+ W L +N NL+ +G F FL AG+ +AQ LI Y+ D++ R + Sbjct: 8 IITVVAVVGMGWYLFDNTQTNLQHRGITSGFDFLERSAGFGIAQHLIDYTESDSYARVFV 67 Query: 90 EGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPLLLWILLMGT 149 GLLNTLLV+ +G ILATILG I+GV RLS+NW++A++ TVYVE FRNIP LL IL Sbjct: 68 IGLLNTLLVTFIGVILATILGFIVGVARLSKNWIIAKLATVYVEVFRNIPPLLQILFWYF 127 Query: 150 ILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFDHSLGVVDLGW 209 + T P P++ S F D+ V++RG N+PA D W Sbjct: 128 AVFLTMPGPRN----------------SHNFGDTFFVSSRGLNMPAAL------AADGFW 165 Query: 210 NLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSL-LILFAP-ISALL 267 S+ +AI+A++ S W +RF EATG +W L L L P + AL+ Sbjct: 166 PFVASI-VVAIVAIVLMSRWATKRF--------EATGVPFHKFWAGLALFLVIPALCALI 216 Query: 268 YGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQTEA 327 +G H + P++ F+F GG+ ++ AL +ALT+YTAAFIAEIVR+GI+++S GQTEA Sbjct: 217 FGAPLHWEMPELKGFNFVGGWVLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEA 276 Query: 328 AYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGITLN 387 A++LGLR G T+ VI+PQALRVI+PPL SQ+LNL KNSSLA + Y ++ G LN Sbjct: 277 AHSLGLRNGPTLRKVIIPQALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLN 336 Query: 388 QTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426 QTG+ +E + + M +YL IS++IS LMN YNK I L ER Sbjct: 337 QTGQAIEVIAITMSVYLAISISISLLMNWYNKRIALIER 375 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: 374 Number of extensions: 12 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 426 Length of database: 375 Length adjustment: 31 Effective length of query: 395 Effective length of database: 344 Effective search space: 135880 Effective search space used: 135880 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