Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate GFF196 PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__Phaeo:GFF196 Length = 432 Score = 291 bits (746), Expect = 2e-83 Identities = 171/434 (39%), Positives = 246/434 (56%), Gaps = 72/434 (16%) Query: 8 FVRTSILAAEPPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAV 67 FVR + + PPP E G WIR NL ++ + ILT+ ALALI + + WL + V Sbjct: 11 FVRETQIPPAPPPGRETGVYKWIRENLFSSVPNSILTLAALALIYALLSSTLPWL-LNGV 69 Query: 68 WSGPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFG-RYPLGERWRPAIVGILFIL 126 W+ C L DG GAC++ ++ +++Q ++G +YP E WRP + +L ++ Sbjct: 70 WTTNSLAECREVL------DGKLGACFSVLTERWNQLLYGFKYPGTEYWRPNLALVLLLV 123 Query: 127 LLVPMLIPSAPRKGLNAILLF-AVLPVIAFWLLHGG------------------------ 161 L P+L PRK +L F A+ P +AFWL+ GG Sbjct: 124 ALAPVLFFDLPRK----LLAFTAIYPFLAFWLIWGGSILVPIVALLGFVAAGFVFQKFGK 179 Query: 162 -------FGLEVVETPLW-------------------------GGLMVTLVLSFVGIAVS 189 FG V +W GG M+ ++L +++S Sbjct: 180 GSFALGFFGAIVAAVVVWNIGGFLIPEGASDNAMLSAVPSRDLGGFMLNMMLGVTCVSLS 239 Query: 190 LPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLR 249 +P+GI LALGR+S MP+I+ +CV FIE +RGVPLIT+LF+ASVML F P VD LR Sbjct: 240 VPLGIALALGRQSNMPLIKWICVVFIEFVRGVPLITLLFVASVMLSYFFPPDATVDLFLR 299 Query: 250 ALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIV 309 +I +++F++AY+AEVIRGGL A+PKGQ+E ADSLGL Y Q RLII+PQA+K+ IP IV Sbjct: 300 VVIMITLFSAAYIAEVIRGGLAALPKGQYEAADSLGLDYPQAMRLIILPQALKISIPGIV 359 Query: 310 NTFIGTFKDTSLVTIIGMFDLLGIVK-LNFSDANWASAVTPITGLIFAGFIFWLFCFGMS 368 N +G FKDT+LV++I MFDL+G+++ + W + G FA F+F++ C+G+S Sbjct: 360 NVAVGLFKDTTLVSVISMFDLVGMIRGPILASTEWNGVYWELLG--FAAFLFFIVCYGIS 417 Query: 369 RYSGFMERHLDTGH 382 +YS ++ER L T H Sbjct: 418 QYSQWLERRLATDH 431 Lambda K H 0.330 0.145 0.469 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: 527 Number of extensions: 38 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 384 Length of database: 432 Length adjustment: 31 Effective length of query: 353 Effective length of database: 401 Effective search space: 141553 Effective search space used: 141553 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 (21.8 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