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 WP_012043999.1 BBTA_RS18360 amino acid ABC transporter permease
Query= TCDB::Q52814 (384 letters) >NCBI__GCF_000015165.1:WP_012043999.1 Length = 506 Score = 278 bits (711), Expect = 2e-79 Identities = 137/233 (58%), Positives = 180/233 (77%), Gaps = 2/233 (0%) Query: 152 VIAFWLLHGGFGLEVVETPLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLC 211 VIA L G GL +V+T LWGG++VTLV+S +GI S+P+GI LALGRRS +P+IR+ Sbjct: 275 VIAIMGLDRG-GLPIVDTRLWGGMLVTLVVSVIGIVASMPIGIALALGRRSTIPLIRLFS 333 Query: 212 VTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQ 271 + FIE++RGVPLITVLF A+ MLPLFLP +D L+RAL+GV++F+ AYMAEVIRGGLQ Sbjct: 334 IAFIELVRGVPLITVLFFATYMLPLFLPGNMRIDGLVRALVGVALFSGAYMAEVIRGGLQ 393 Query: 272 AIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLL 331 AIP+GQ E A +LGL +W+ T I++PQA++ VIP IVN+FI FKDTSLV+I+ +FDLL Sbjct: 394 AIPRGQAEAASALGLSWWKTTSFIVLPQALRHVIPGIVNSFISLFKDTSLVSIVALFDLL 453 Query: 332 GIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYSGFMERHLDTGHKR 384 G +K +F+D WA+ T TG F G I+++FCFGMSRYS +ER L+ H+R Sbjct: 454 GSLKASFADPVWATPTTAFTGFAFTGLIYFVFCFGMSRYSLLVERRLN-AHRR 505 Score = 123 bits (309), Expect = 1e-32 Identities = 113/393 (28%), Positives = 178/393 (45%), Gaps = 57/393 (14%) Query: 8 FVRTSILAAEPPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAV 67 F+R + P P G ++R LL +P +++LT+++ LI + V + +L + AV Sbjct: 9 FIRQDMAGERPAPVKTTGFTGFVRTRLLNSPTNILLTLVSALLIWFTVIPALKFLLVDAV 68 Query: 68 WSGPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILL 127 W G DR C G GACW +++AK+ QF++G YP ERWR + L ++L Sbjct: 69 WVGKDREACLEQNVGHAV-----GACWPYVTAKFGQFMYGFYPDAERWRVNLTYGLAVVL 123 Query: 128 LVPMLIPSAPRKGLNAILLFAVLPVIAFWLLHG----GFGLEVVETPLWGGLMVTLVLSF 183 LVP+LIP P KGLNA L F LPV+AF+LL+G GFG+ W + L Sbjct: 124 LVPLLIPRLPAKGLNAGLFFFALPVVAFFLLYGGGLSGFGVS------WTAATLQLFAES 177 Query: 184 VGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWN 243 V A G L G + +PV+ ML + G ++ + +AS+ L P W Sbjct: 178 VDTA-----GNALVRG-GANLPVVGMLM-----WLLGKLVVLIGMLASL---LIWPLVWV 223 Query: 244 VDKLLRAL------IGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIM 297 D+L + + ++ + VI GG +A+ A G+ L+I Sbjct: 224 RDQLQASHQPVWTDLALTAIVVTALVFVIGGGSRALRSVVATAATFAGIA------LVIA 277 Query: 298 PQAIKLVIPSIVNTFI-GTFKDTSLVTIIGMF--------------DLLGIVKL-NFSDA 341 + IV+T + G T +V++IG+ + +++L + + Sbjct: 278 IMGLDRGGLPIVDTRLWGGMLVTLVVSVIGIVASMPIGIALALGRRSTIPLIRLFSIAFI 337 Query: 342 NWASAVTPITGLIFAGFIFWLFCFGMSRYSGFM 374 V IT L FA ++ LF G R G + Sbjct: 338 ELVRGVPLITVLFFATYMLPLFLPGNMRIDGLV 370 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: 693 Number of extensions: 34 Number of successful extensions: 3 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: 506 Length adjustment: 32 Effective length of query: 352 Effective length of database: 474 Effective search space: 166848 Effective search space used: 166848 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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