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 17341 b3271 predicted amino-acid transporter subunit (NCBI)
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__Keio:17341 Length = 252 Score = 234 bits (597), Expect = 1e-66 Identities = 123/251 (49%), Positives = 166/251 (66%), Gaps = 11/251 (4%) Query: 4 ATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQ 63 A + + N++K YG VLK I+LT + G+ I + G SGSGKST +RCIN LE QG+ Sbjct: 9 ANAMITLENVNKWYGQFHVLKNINLTVQPGERIVLCGPSGSGKSTTIRCINHLEEHQQGR 68 Query: 64 ILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVL 123 I+V G EL D + I R+R E+G VFQ+FNL+PH+++L N AP V Sbjct: 69 IVVDGIELN-----------EDIRNIERVRQEVGMVFQHFNLFPHLTVLQNCTLAPIWVR 117 Query: 124 GKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183 K EA ++A L +V IA+ H +P Q+SGGQQQR AIAR+L M+PK++LFDEPTSA Sbjct: 118 KMPKKEAEDLAVHYLERVRIAEHAHKFPGQISGGQQQRVAIARSLCMKPKIMLFDEPTSA 177 Query: 184 LDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFEN 243 LDPEMV+EVL+ + LA+ G TML VTHEM FAR V+ V+F+ +G + EQ P + F + Sbjct: 178 LDPEMVKEVLDTMIGLAQSGMTMLCVTHEMGFARTVADRVIFMDRGEIVEQAAPDEFFAH 237 Query: 244 PQSARCKQFMS 254 P+S R + F+S Sbjct: 238 PKSERTRAFLS 248 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: 152 Number of extensions: 2 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: 252 Length adjustment: 24 Effective length of query: 233 Effective length of database: 228 Effective search space: 53124 Effective search space used: 53124 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