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 YP_001328644.1 Smed_2980 polar amino acid ABC transporter inner membrane subunit
Query= TCDB::Q52814 (384 letters) >NCBI__GCF_000017145.1:YP_001328644.1 Length = 223 Score = 111 bits (278), Expect = 2e-29 Identities = 72/214 (33%), Positives = 110/214 (51%), Gaps = 12/214 (5%) Query: 171 LWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMA 230 LWG L VTL + I L G+ LA+ R P + L T+++V R +PL+ +L + Sbjct: 21 LWG-LAVTLQIGITSILCGLAGGLFLAVARLYSPPFCQFLIRTYVDVFRSIPLLVLLIVV 79 Query: 231 SVMLPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQ 290 LP G + L A+ +S+ ++AY AE+ R G++AIP GQFE + +LGL Sbjct: 80 YYALPF---VGIRLSPFLSAVTSLSLVSAAYTAEIFRAGIEAIPHGQFEASAALGLSNRH 136 Query: 291 KTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTP- 349 +I+PQA+++VIP + N I KDT+L +++ M DLL A A A+ Sbjct: 137 TMVDVILPQAVRIVIPPLTNNCINVLKDTALASVVAMPDLL-------KQATQAQALAAN 189 Query: 350 ITGLIFAGFIFWLFCFGMSRYSGFMERHLDTGHK 383 T LI A I+ + + M G +E G + Sbjct: 190 PTPLIGAAIIYVMLLWPMVIVVGRLETIFSRGRR 223 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: 221 Number of extensions: 15 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: 223 Length adjustment: 26 Effective length of query: 358 Effective length of database: 197 Effective search space: 70526 Effective search space used: 70526 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: 48 (23.1 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