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 5209222 Shew_1700 phosphate ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q52815 (257 letters) >FitnessBrowser__PV4:5209222 Length = 272 Score = 137 bits (345), Expect = 2e-37 Identities = 82/252 (32%), Positives = 145/252 (57%), Gaps = 11/252 (4%) Query: 11 VSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEE-- 68 +S+ + A+EI N++ YGD L D+++K+ + + GPSG GKST++RCINR+ + Sbjct: 19 LSSEQTALEIRNLDLKYGDKQALFDVSMKIPKKKVTAFIGPSGCGKSTLLRCINRMNDLV 78 Query: 69 ---HQKGKIVVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMP 125 + G+I++ G + + + +RR VGMVFQ N FP +I EN Sbjct: 79 DNCNIDGEILLHGQNIYDKKVDVASLRRNVGMVFQRPNPFPK-SIYENVVYGLRLQGINN 137 Query: 126 KKQAEEVAMHFLKRV----KIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTS 181 ++Q +E A L+ ++ ++ + LSGGQQQR+ IAR++ + P+++L DEPTS Sbjct: 138 RRQLDEAAERSLRGAAIWDEVKDRLHDNAFGLSGGQQQRLVIARAIAIEPEVLLLDEPTS 197 Query: 182 ALDPEMIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFD 241 ALDP + ++ ++ + T++ VTH M A +V+++ FM G++VE + F Sbjct: 198 ALDP-ISTLTIEELITELKAKYTVVIVTHNMQQAARVSDQTAFMYMGELVEYADTNTIFT 256 Query: 242 NPQHERTKLFLS 253 P+ ++T+ +++ Sbjct: 257 TPKKKKTEDYIT 268 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: 168 Number of extensions: 9 Number of successful extensions: 4 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: 272 Length adjustment: 25 Effective length of query: 232 Effective length of database: 247 Effective search space: 57304 Effective search space used: 57304 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