Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate PfGW456L13_1699 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1699 Length = 393 Score = 304 bits (778), Expect = 4e-87 Identities = 182/421 (43%), Positives = 254/421 (60%), Gaps = 37/421 (8%) Query: 8 PKAGFRLSMLIYDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRA 67 PK LS D R R+ QI+ ++ ++ +L +N NL+ +G F FL A Sbjct: 8 PKQRLSLS----DPRVRAWVFQIITIIAVVSLGWYLFDNTQTNLQHRGITSGFDFLERSA 63 Query: 68 GYDLAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARI 127 G+ +AQ LI Y+ DT+ R + GLLNTLLV+ +G ILATILG I+GV RLS+NW++A++ Sbjct: 64 GFGIAQHLIDYTEADTYARVFVIGLLNTLLVTFIGVILATILGFIVGVARLSKNWIIAKL 123 Query: 128 MTVYVETFRNIPLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVT 187 TVYVE FRNIP LL IL + T P P++ S F D+ V+ Sbjct: 124 ATVYVEVFRNIPPLLQILFWYFAVFLTMPGPRN----------------SHNFGDTFFVS 167 Query: 188 NRGTNLPAPAFDHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGT 247 +RG N+PA + D W S+ +AI+A++ S W +RF EATG Sbjct: 168 SRGLNMPAAL------MADGFWPFMTSV-VVAIVAIVLMSRWATKRF--------EATGV 212 Query: 248 RPTTWWPSL--LILFAPISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYT 305 +W L ++ + AL++G H + P++ F+F GG+ ++ AL +ALT+YT Sbjct: 213 PFHKFWVGLAMFLVIPALCALIFGAPVHWEMPKLQGFNFVGGWVLIPELLALTLALTVYT 272 Query: 306 AAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKN 365 AAFIAEIVR+GI+++S GQTEAA++LGLR G T+ VI+PQALRVI+PPL SQ+LNL KN Sbjct: 273 AAFIAEIVRSGIKSVSHGQTEAAHSLGLRNGPTLRKVIIPQALRVIIPPLTSQYLNLAKN 332 Query: 366 SSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKE 425 SSLA + Y ++ G LNQTG+ +E + + M +YL IS++IS LMN YNK I L E Sbjct: 333 SSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLLMNWYNKRIALIE 392 Query: 426 R 426 R Sbjct: 393 R 393 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: 395 Number of extensions: 13 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: 393 Length adjustment: 31 Effective length of query: 395 Effective length of database: 362 Effective search space: 142990 Effective search space used: 142990 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