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 GFF2244 HP15_2194 amino acid ABC transporter, permease protein
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__Marino:GFF2244 Length = 362 Score = 370 bits (951), Expect = e-107 Identities = 193/359 (53%), Positives = 252/359 (70%), Gaps = 16/359 (4%) Query: 27 VAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVWSGPDRTFCATTLQGGIQP 86 V W+R NL + + +LT+ L+ +V L+NW F+ A + G D + C Sbjct: 17 VKWMRENLFSGWFNTVLTLGVAYLLVTSVGPLLNWFFLDANFVGSDPSACTG-------- 68 Query: 87 DGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILLLVPMLIPSAP-RKGLNAIL 145 +GACW FIS + + FI+G YP +WR ++ +L + VP I P RK L Sbjct: 69 ---AGACWLFISQRLNFFIYGFYPDELQWRVDVMFLLLAVSFVPQFIERFPGRKWLGLFG 125 Query: 146 LFAVLPVIAFWLLHGG-FGLEVVETPLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRM 204 +F LP++ ++L+ GG FGLE V++ WGGLM+TL+L+++GI SLP+GILLALGRRS M Sbjct: 126 IFG-LPIVGYFLIPGGSFGLEEVQSSKWGGLMLTLILAYIGIIASLPIGILLALGRRSDM 184 Query: 205 PVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLRALIGVSIFTSAYMAE 264 P+IR +CV FIEV R VPLITVLFMASVMLPLFLP G N +KL RALIG++++ SAYMAE Sbjct: 185 PIIRGICVVFIEVWRAVPLITVLFMASVMLPLFLPEGVNFEKLARALIGITLWQSAYMAE 244 Query: 265 VIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTI 324 VIRGGLQAIP+GQ+E AD+LGLGYW+K L+I+PQA+K+VIP IVNTFI FKDT+LV I Sbjct: 245 VIRGGLQAIPRGQYEAADALGLGYWRKMGLVILPQALKMVIPGIVNTFISLFKDTTLVLI 304 Query: 325 IGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYSGFMERHLDTGHK 383 IG+FD+LG V+ +D W + I G +F F FW+FCFG+SRYS +ER LDTGHK Sbjct: 305 IGLFDILGTVQSTVTDPAWQNVA--IEGYVFVAFCFWVFCFGISRYSQNLERKLDTGHK 361 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: 595 Number of extensions: 35 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: 362 Length adjustment: 30 Effective length of query: 354 Effective length of database: 332 Effective search space: 117528 Effective search space used: 117528 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