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_012384589.1 BIND_RS08110 amino acid ABC transporter permease
Query= TCDB::Q52814 (384 letters) >NCBI__GCF_000019845.1:WP_012384589.1 Length = 385 Score = 346 bits (887), Expect = e-100 Identities = 186/375 (49%), Positives = 243/375 (64%), Gaps = 19/375 (5%) Query: 18 PPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVWSGPDRTFCA 77 PPP + IRR ++ +LT+ A ALI W +P L+ + I AVWS PD C Sbjct: 22 PPPKDRTSLLERIRRGFFSSLSSSLLTLAAGALILWLLPDLLRFTLIDAVWSAPDGAACR 81 Query: 78 TTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILLLVPMLIPSAP 137 PD +GACWAF++ K F FG YP+ ERWR V +L +L+ +L P Sbjct: 82 A-------PD--AGACWAFVAQKLPYFTFGSYPVAERWRVVTVLLLGFVLIAWLLWPI-- 130 Query: 138 RKGLN------AILLFAVLPVIAFWLLHGG--FGLEVVETPLWGGLMVTLVLSFVGIAVS 189 RKG + A+L F + P+IA LL G GL +V+T LWGG+ ++LV++ VGI VS Sbjct: 131 RKGAHTDKRVAALLFFLLYPLIALILLRGTPWLGLPLVDTDLWGGIFLSLVVAGVGIVVS 190 Query: 190 LPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLR 249 LP+GI LALGRRS +PV+ + FIE +RGVP+ITVLFMA+ MLPLFLP +VD+L+R Sbjct: 191 LPLGIFLALGRRSTLPVVSLASTLFIEFVRGVPMITVLFMANFMLPLFLPASMSVDRLIR 250 Query: 250 ALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIV 309 LIGV++F SAYMAEV+RGGLQA+PKGQFEGA +LGL W+ +L+++PQA+ VIP IV Sbjct: 251 PLIGVALFASAYMAEVVRGGLQAVPKGQFEGAAALGLPPWKTLQLVVLPQALAHVIPGIV 310 Query: 310 NTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSR 369 NTFIG FKDT+LV +G+FD L V D WA +G +FA +++FCFGMSR Sbjct: 311 NTFIGLFKDTTLVAAVGIFDFLRTVDSARLDPAWAGPTISASGYLFAALFYFVFCFGMSR 370 Query: 370 YSGFMERHLDTGHKR 384 YS +ER L G R Sbjct: 371 YSIGVERRLARGQAR 385 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: 561 Number of extensions: 32 Number of successful extensions: 3 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: 385 Length adjustment: 30 Effective length of query: 354 Effective length of database: 355 Effective search space: 125670 Effective search space used: 125670 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 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