Align AapP, 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 PfGW456L13_446 Cystine ABC transporter, ATP-binding protein
Query= TCDB::Q52815 (257 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_446 Length = 251 Score = 236 bits (601), Expect = 4e-67 Identities = 127/246 (51%), Positives = 162/246 (65%), Gaps = 6/246 (2%) Query: 18 VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77 + + + K + VL I+L+V GE + I GPSGSGK+T +RC+N LEE G+I V Sbjct: 2 IVVEKLTKQFKGQIVLNGIDLEVKEGEVVAIIGPSGSGKTTFLRCLNFLEEPTSGRIKVG 61 Query: 78 GTE------LTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEE 131 E L + +R+ VG VFQ+FNLFPH T LEN PI V+K P A Sbjct: 62 DIEVDTSRPLNQQQSLVRRLRQHVGFVFQNFNLFPHRTALENVIEGPIVVKKTPHADAVA 121 Query: 132 VAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEV 191 + L +V + + + YP +LSGGQQQRVAIAR+L M P+++LFDEPTSALDPE++ EV Sbjct: 122 LGKKLLAKVGLAGKEDAYPRRLSGGQQQRVAIARALAMEPEVILFDEPTSALDPELVGEV 181 Query: 192 LDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLF 251 L T+ GLAEE TM+ VTHEMGFAR VANRV+F D+G IVEQ E A F NP+ ERTK F Sbjct: 182 LATIRGLAEEKRTMVIVTHEMGFARDVANRVVFFDKGVIVEQGEAKALFANPKEERTKQF 241 Query: 252 LSQILH 257 LS+ L+ Sbjct: 242 LSKFLN 247 Lambda K H 0.321 0.135 0.394 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: 210 Number of extensions: 6 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: 257 Length of database: 251 Length adjustment: 24 Effective length of query: 233 Effective length of database: 227 Effective search space: 52891 Effective search space used: 52891 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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