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 WP_084057089.1 B9A12_RS06595 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52812 (341 letters) >NCBI__GCF_900176285.1:WP_084057089.1 Length = 337 Score = 378 bits (970), Expect = e-109 Identities = 190/329 (57%), Positives = 234/329 (71%), Gaps = 3/329 (0%) Query: 13 AVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFDVDFCKAVASAVF 72 AVLA+ A ASA TL +V+A+G++ GVN + GF+ PD G W G DVD +A+A+AVF Sbjct: 12 AVLAL-ALPASAGTLDEVRARGYLIAGVNGSVFGFSMPDEKGVWKGLDVDTARAIAAAVF 70 Query: 73 GDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRPVTYYDGQGFMVR 132 GD +KVK+ P A +R ALQS EIDVL RNTT T+ R+T G NF V +YDGQGF+V Sbjct: 71 GDASKVKFVPLTAVQRLPALQSKEIDVLCRNTTQTLTRETTNGLNFVHVNFYDGQGFLVP 130 Query: 133 KGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLPEVNAAYDAGRCD 192 K L +KSA EL GA +CV GTTTELN AD+F+ NN+Q+ PVV E E+N A+ AGRCD Sbjct: 131 KKLGIKSAKELDGATVCVLPGTTTELNAADFFRKNNMQWKPVVIEQAAELNKAFFAGRCD 190 Query: 193 VYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDIVSWTAYALINAE 252 V T+D S L R NPD++++LPEIISKEPL P VR GDDQW+DIV+WT ALI AE Sbjct: 191 VLTSDSSQLAGHRAVAPNPDDYVLLPEIISKEPLAPVVRHGDDQWYDIVNWTVMALIQAE 250 Query: 253 EFGITQANVDEMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVIKGVGNYGEIFERN 312 EFGIT NVDEM S +P I+RFLG +G LGL + W N+IK VGNYGEI+ERN Sbjct: 251 EFGITSKNVDEMLKSKDPAIQRFLG--VTPGMGKALGLDDKWTYNIIKQVGNYGEIYERN 308 Query: 313 IGQGSPLKIARGLNALWNKGGIQYAPPVR 341 +G +PL + RGLNALW +GG+ YA P R Sbjct: 309 VGPNTPLGMPRGLNALWTQGGLMYAAPFR 337 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: 354 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: 341 Length of database: 337 Length adjustment: 28 Effective length of query: 313 Effective length of database: 309 Effective search space: 96717 Effective search space used: 96717 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