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_004143816.1 Mesci_4657 cationic amino acid ABC transporter periplasmic binding protein
Query= TCDB::Q52812 (341 letters) >NCBI__GCF_000185905.1:YP_004143816.1 Length = 342 Score = 531 bits (1368), Expect = e-156 Identities = 251/334 (75%), Positives = 290/334 (86%), Gaps = 2/334 (0%) Query: 10 IGAAVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFDVDFCKAVAS 69 +GAA L + ASAASA TL VKAKGF+QCGV+TGL GF+APD G+W G D DFC+AVA+ Sbjct: 9 LGAATLGLMASAASAATLDTVKAKGFIQCGVSTGLAGFSAPDDKGDWQGIDADFCRAVAA 68 Query: 70 AVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRPVTYYDGQGF 129 AVFGD ++VK+TP +AKERFTALQSGEID+LSRNTTWTINRDTALG NF VTYYDGQGF Sbjct: 69 AVFGDGSRVKFTPLSAKERFTALQSGEIDILSRNTTWTINRDTALGLNFIGVTYYDGQGF 128 Query: 130 MV--RKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLPEVNAAYD 187 M+ +K V SAL+LSGAA+CVQSGTTTELNLADYFK N ++YNPVVFE L EVNAAYD Sbjct: 129 MINAKKLPGVNSALQLSGAAVCVQSGTTTELNLADYFKANKMEYNPVVFEKLEEVNAAYD 188 Query: 188 AGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDIVSWTAYA 247 AGRCDVYTTDQSGLY +RLTL +P +H++LPEIISKEPLGPAVRQGDDQW+ IV WT +A Sbjct: 189 AGRCDVYTTDQSGLYGIRLTLGSPADHVVLPEIISKEPLGPAVRQGDDQWYHIVKWTYFA 248 Query: 248 LINAEEFGITQANVDEMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVIKGVGNYGE 307 L+ AEE GIT+ANVDEMKNS +P+IKR LG E DTKIGTDLG++NDW N++K VGNYGE Sbjct: 249 LLQAEELGITKANVDEMKNSASPEIKRVLGQEADTKIGTDLGVSNDWVVNIVKAVGNYGE 308 Query: 308 IFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341 +FERN+G GSPLKIARG+NALW KGG+QYAPP+R Sbjct: 309 MFERNVGSGSPLKIARGINALWTKGGLQYAPPIR 342 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: 464 Number of extensions: 16 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: 342 Length adjustment: 29 Effective length of query: 312 Effective length of database: 313 Effective search space: 97656 Effective search space used: 97656 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