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 AZOBR_RS08670 AZOBR_RS08670 arginine ABC transporter ATP-binding protein
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__azobra:AZOBR_RS08670 Length = 258 Score = 247 bits (631), Expect = 2e-70 Identities = 132/253 (52%), Positives = 173/253 (68%), Gaps = 11/253 (4%) Query: 2 AEATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQ 61 A+ P ++ + +HK YG+ VLK I L+ G+ I I G SGSGKST +RC+N LE + Sbjct: 12 AQGEPIIQCQGVHKWYGEFHVLKNIDLSVAKGERIVICGPSGSGKSTMIRCLNRLEEHQK 71 Query: 62 GQILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRR 121 G I+V G EL G+L + I +R E+G VFQ+FNL+PH+++L+N AP Sbjct: 72 GSIVVDGIEL------TGNL-----KNIELVRREVGMVFQHFNLFPHLTVLENCTLAPIW 120 Query: 122 VLGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPT 181 V K KAEA E+A L +V IA++ H YP QLSGGQQQR AIAR+L M PKV+LFDEPT Sbjct: 121 VRKKPKAEAEEMAMRYLKRVRIAEQAHKYPGQLSGGQQQRVAIARSLCMSPKVMLFDEPT 180 Query: 182 SALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVF 241 SALDPEMV+EVL+V+ LAE+G TML VTHEM FA+ V+ V+F+ +G + EQ TP + F Sbjct: 181 SALDPEMVKEVLDVMIGLAEDGMTMLCVTHEMGFAKSVADRVIFMDRGEIVEQNTPNEFF 240 Query: 242 ENPQSARCKQFMS 254 +PQS R K F+S Sbjct: 241 NHPQSDRTKLFLS 253 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: 165 Number of extensions: 3 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: 258 Length adjustment: 24 Effective length of query: 233 Effective length of database: 234 Effective search space: 54522 Effective search space used: 54522 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