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 206399 DVU0967 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= TCDB::Q52814 (384 letters) >MicrobesOnline__882:206399 Length = 337 Score = 116 bits (291), Expect = 8e-31 Identities = 65/209 (31%), Positives = 119/209 (56%), Gaps = 11/209 (5%) Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFM---- 229 GL +TL +S + I + + +G++ L R S P +R L +T+IE+IRG PL+ +F+ Sbjct: 130 GLWITLEVSMLAIIIGIVLGVVTGLARISVNPALRWLAITYIEIIRGSPLLVQVFLWYFV 189 Query: 230 -ASVMLPLFLPTGWN-VDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLG 287 +++ LF G + + L ++ ++IFT AY+AE++R G+Q++ +GQ E A SLG+ Sbjct: 190 VGTLLNALFEKVGLSAIPPLWYGVMALAIFTGAYVAEIVRAGIQSVHRGQMEAARSLGMS 249 Query: 288 YWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAV 347 Y Q R +I+PQA + ++P + FI KD+SL+ +I + +L + + +++ Sbjct: 250 YAQSMRKVILPQAFRRIMPPLAGQFISLVKDSSLLGVIAVRELTKATREVVT-----TSL 304 Query: 348 TPITGLIFAGFIFWLFCFGMSRYSGFMER 376 P I ++ + F +S ++ER Sbjct: 305 QPFELWIVCALLYLVLTFTLSLCVQYLER 333 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: 350 Number of extensions: 17 Number of successful extensions: 2 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: 337 Length adjustment: 29 Effective length of query: 355 Effective length of database: 308 Effective search space: 109340 Effective search space used: 109340 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: 49 (23.5 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