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 RR42_RS29660 RR42_RS29660 amino acid transporter
Query= TCDB::Q52815 (257 letters) >FitnessBrowser__Cup4G11:RR42_RS29660 Length = 264 Score = 237 bits (604), Expect = 2e-67 Identities = 126/256 (49%), Positives = 171/256 (66%), Gaps = 12/256 (4%) Query: 10 TVSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEH 69 T A + + +++K +GD VL+ ++L +G+ I I G SGSGKST +RCIN LE Sbjct: 5 TTQAMSCKLAVQDIHKSFGDNEVLKGVSLTAKKGDVISIIGASGSGKSTFLRCINYLERP 64 Query: 70 QKGKIVVDGTEL------TNDL-----KKIDEVRREVGMVFQHFNLFPHLTILENCTLAP 118 + G+I +DG E+ T DL K++ +R ++ MVFQHFNL+ H+ +LEN AP Sbjct: 65 KSGQIFLDGEEIRTKKDKTGDLVVVEPKQLQRMRTKLSMVFQHFNLWAHMNVLENIIEAP 124 Query: 119 IWVRKMPKKQAEEVAMHFLKRVKIPEQANK-YPGQLSGGQQQRVAIARSLCMNPKIMLFD 177 V + +K+AEE A +L++V +P + K YP LSGGQQQRVAIAR+L MNP +MLFD Sbjct: 125 THVLGLSRKEAEERAREYLEKVGLPPRVEKQYPSHLSGGQQQRVAIARALAMNPDVMLFD 184 Query: 178 EPTSALDPEMIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPA 237 EPTSALDPE++ EVL M LAEEG TM+ VTHEMGFAR V+N V+F+ QG+ EQ P Sbjct: 185 EPTSALDPELVGEVLKVMQKLAEEGRTMIVVTHEMGFARNVSNHVMFLHQGRTEEQGPPE 244 Query: 238 AFFDNPQHERTKLFLS 253 ++P+ ER + FLS Sbjct: 245 EVLNSPRSERLRQFLS 260 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: 199 Number of extensions: 6 Number of successful extensions: 3 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: 264 Length adjustment: 25 Effective length of query: 232 Effective length of database: 239 Effective search space: 55448 Effective search space used: 55448 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