Align AapJ, 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_004141767.1 Mesci_2581 family 3 extracellular solute-binding protein
Query= TCDB::Q52812 (341 letters) >NCBI__GCF_000185905.1:YP_004141767.1 Length = 344 Score = 273 bits (698), Expect = 5e-78 Identities = 144/338 (42%), Positives = 200/338 (59%), Gaps = 4/338 (1%) Query: 1 MKNKLLSAAIGAAVLAVGASAASATTLSDVKAKGFVQC-GVNTGLTGFAAPDASGNWAGF 59 MK + A+G A A AA TL VKA+G + C G + GFA D GNW G Sbjct: 4 MKWGAAAMALGLVHFAAPAEAAGGKTLEAVKARGVLNCTGHDGSYLGFAEVDDKGNWKGM 63 Query: 60 DVDFCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFR 119 D+D C+AVA+AV GDP K+K P + +R+ +LQSG++D++ + + T++RDT LG F Sbjct: 64 DIDLCRAVATAVLGDPAKLKVVPISWAQRWPSLQSGDVDIIIKASGGTLSRDTELGLQFS 123 Query: 120 PVTYYDGQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENL 179 Y M K LN+KS + +G IC+ +GT+ E +A Y ++ PV+ E Sbjct: 124 MSYYLGTTKVMAHKELNLKSLKDAAGGTICIPAGTSQEQQVAAYTAKLGIKLEPVLIEKT 183 Query: 180 PEVNAAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFD 239 E+ AY +GRCD+Y L R+ D+H+ILP++++ EP +RQGDD W D Sbjct: 184 EELEQAYFSGRCDLYAQWGPTLAIARIAKSKVDDHVILPDVLAVEPEVMIMRQGDDNWVD 243 Query: 240 IVSWTAYALINAEEFGITQANVDEMKNSP-NPDIKRFLGSETDTKIGTDLGLTNDWAANV 298 I +WT LI AE+ GIT NVDE+K P +P + +FLG +G LGL +DWA V Sbjct: 244 IANWTLSTLIFAEQEGITSKNVDEVKAKPTSPQVAKFLG--VTPGMGKGLGLDDDWAYKV 301 Query: 299 IKGVGNYGEIFERNIGQGSPLKIARGLNALWNKGGIQY 336 IK VGNYGEIFER++G+ SP K+ R L LWN GG+ + Sbjct: 302 IKNVGNYGEIFERDLGKDSPYKMDRELTNLWNNGGVLF 339 Lambda K H 0.316 0.134 0.398 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: 328 Number of extensions: 13 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: 341 Length of database: 344 Length adjustment: 29 Effective length of query: 312 Effective length of database: 315 Effective search space: 98280 Effective search space used: 98280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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