Align Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate 7025581 Shewana3_2732 phosphate ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__ANA3:7025581 Length = 272 Score = 140 bits (353), Expect = 3e-38 Identities = 98/263 (37%), Positives = 142/263 (53%), Gaps = 22/263 (8%) Query: 1 MAEATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCIN----LL 56 +++ ALEIRNL RYGD + L +S+ V + +G SG GKST LRCIN L+ Sbjct: 19 LSQNDTALEIRNLDLRYGDKQALFNVSMKIPKKQVTAFIGPSGCGKSTLLRCINRMNDLV 78 Query: 57 ENPH-QGQILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNV 115 +N H G+IL+ G+ + KK VAA LR +G VFQ N +P SI +NV Sbjct: 79 DNCHIDGEILLHGQNIYDKKID----VAA-------LRRNVGMVFQRPNPFPK-SIYENV 126 Query: 116 IEAPRRVLGKSKAEAIEIAEGLLAKVGI----ADKRHSYPAQLSGGQQQRAAIARTLAMQ 171 + R ++ E E AE L I D+ H LSGGQQQR IAR +A++ Sbjct: 127 VYGLRLQGINNRRELDEAAERSLRGAAIWDEVKDRLHDNAFGLSGGQQQRLVIARAIAIE 186 Query: 172 PKVILFDEPTSALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLV 231 P+V+L DEPTSALDP + +I L + T+++VTH M A +VS + F++ G + Sbjct: 187 PEVLLLDEPTSALDPISTLTIEELITELKTK-YTVVIVTHNMQQAARVSDQTAFMYMGEL 245 Query: 232 EEQGTPQQVFENPQSARCKQFMS 254 E +F P+ + + +++ Sbjct: 246 VEYADTNTIFTTPKKRKTEDYIT 268 Lambda K H 0.317 0.133 0.367 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: 135 Number of extensions: 5 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: 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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