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 17340 b3270 putative transport system permease protein (VIMSS)
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__Keio:17340 Length = 367 Score = 363 bits (931), Expect = e-105 Identities = 184/375 (49%), Positives = 250/375 (66%), Gaps = 17/375 (4%) Query: 11 TSILAAEPPPPGERG---AVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAV 67 T +L + PP P A+ W+R+NL ++ + +LTI + L+ +P L+NW F+QA Sbjct: 2 TKVLLSHPPRPASHNSSRAMVWVRKNLFSSWSNSLLTIGCIWLMWELIPPLLNWAFLQAN 61 Query: 68 WSGPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILL 127 W G R C +GACW FI ++ QF++G YP +RWR + ++ ++ Sbjct: 62 WVGSTRADCTK-----------AGACWVFIHERFGQFMYGLYPHDQRWRINLALLIGLVS 110 Query: 128 LVPMLIPSAPRKGLNAILLFAVLPVIAFWLLHGGF-GLEVVETPLWGGLMVTLVLSFVGI 186 + PM P +G + P+I +WL++GGF LE VET WGGL +TL+++ VGI Sbjct: 111 IAPMFWKILPHRGRYIAAWAVIYPLIVWWLMYGGFFALERVETRQWGGLTLTLIIASVGI 170 Query: 187 AVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDK 246 A +LP GILLALGRRS MP++R+L V FIE RGVPLITVLFM+SVMLPLF+ G ++DK Sbjct: 171 AGALPWGILLALGRRSHMPIVRILSVIFIEFWRGVPLITVLFMSSVMLPLFMAEGTSIDK 230 Query: 247 LLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIP 306 L+RAL+GV +F SAY+AEV+RGGLQA+PKGQ+E A+SL LGYW+ L+I+PQA+KLVIP Sbjct: 231 LIRALVGVILFQSAYVAEVVRGGLQALPKGQYEAAESLALGYWKTQGLVILPQALKLVIP 290 Query: 307 SIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFG 366 +VNT I FKDTSLV IIG+FDL V+ D W T G +FA I+W+FCF Sbjct: 291 GLVNTIIALFKDTSLVIIIGLFDLFSSVQQATVDPAWLGMST--EGYVFAALIYWIFCFS 348 Query: 367 MSRYSGFMERHLDTG 381 MSRYS ++E+ +TG Sbjct: 349 MSRYSQYLEKRFNTG 363 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: 564 Number of extensions: 26 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: 384 Length of database: 367 Length adjustment: 30 Effective length of query: 354 Effective length of database: 337 Effective search space: 119298 Effective search space used: 119298 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