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_110804794.1 C8J30_RS05895 amino acid ABC transporter permease
Query= TCDB::Q52814 (384 letters) >NCBI__GCF_003217355.1:WP_110804794.1 Length = 434 Score = 293 bits (751), Expect = 5e-84 Identities = 180/438 (41%), Positives = 241/438 (55%), Gaps = 61/438 (13%) Query: 3 VADKPFVRTSILAAEPPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWL 62 ++D FVRT +L +P P + G V W+R NL + P + LT+ L + AW V WL Sbjct: 1 MSDTSFVRTEMLPPKPAPVSQVGVVKWMRENLFSGPLNTALTVFGLLVTAWLVQAGAPWL 60 Query: 63 FIQAVWSGPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGI 122 I VW+ T C T + P+ +GACWA I +++QF+FG YP+ E WR + Sbjct: 61 -IHGVWNANSLTECRTIIAERWGPEA-TGACWAIIRVRWNQFLFGFYPVEEYWRLFLTFA 118 Query: 123 LFILLLVPMLIPSAPRKGLNAILLFAVL-------------------------------- 150 L L P+L + PRK + LL+ ++ Sbjct: 119 GLFLALAPVLFDALPRKLIWGTLLYPLVAFWLLWGGPVWGPVGVLVGFALMGLAFTRLAP 178 Query: 151 ----PVIA---------FWLLHGG-----------FGLEVVETPLWGGLMVTLVLSFVGI 186 PV A WL G L V + +GG ++ LV+ I Sbjct: 179 KLGVPVAAGAGLILAAVVWLYAVGPFESAMQSVLPLALPEVVSDKFGGFLLALVIGVTAI 238 Query: 187 AVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDK 246 VSLP+GILLALGR+S M +++ L V IE IRGVPLIT+LF AS++L FLP G D Sbjct: 239 VVSLPLGILLALGRQSDMVMVKALSVGMIEFIRGVPLITLLFTASLLLQYFLPPGTTFDL 298 Query: 247 LLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIP 306 +LR +I V++F +AY+AEVIRGGL A+P+GQ+E AD+LGL YWQ RLIIMPQA+K+ IP Sbjct: 299 ILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIP 358 Query: 307 SIVNTFIGTFKDTSLVTIIGMFD-LLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCF 365 IV++FIG FKDT+LVT +G+FD L GI + SD W T IF IF+LF F Sbjct: 359 GIVSSFIGLFKDTTLVTFVGLFDPLKGISGVVRSDMAWKG--TYWEPYIFVAVIFFLFNF 416 Query: 366 GMSRYSGFMERHLDTGHK 383 MSRYS ++ER L H+ Sbjct: 417 SMSRYSMYLERKLKRDHR 434 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: 635 Number of extensions: 48 Number of successful extensions: 5 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: 434 Length adjustment: 31 Effective length of query: 353 Effective length of database: 403 Effective search space: 142259 Effective search space used: 142259 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