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 WP_076948807.1 C1M55_RS07375 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q9HU32 (257 letters) >NCBI__GCF_002893965.1:WP_076948807.1 Length = 261 Score = 247 bits (630), Expect = 2e-70 Identities = 127/252 (50%), Positives = 169/252 (67%), Gaps = 1/252 (0%) Query: 3 EATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQG 62 E A+E R +HK +G LEVL G+ L R G+V ILG SGSGKST LR +N LE +G Sbjct: 8 ETVYAVEARGIHKSFGTLEVLAGVDLLVRKGEVTVILGPSGSGKSTLLRTLNHLEKVDRG 67 Query: 63 QILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRV 122 + + GE + ++ K L ++I + RS +GFVFQNFNL+PH++ L+NV+EAP Sbjct: 68 TVRIDGELIGYRR-KGNRLHELRDREILKQRSHIGFVFQNFNLFPHLTALENVVEAPLSA 126 Query: 123 LGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTS 182 + + E A LL +VG+ +K YP QLSGGQQQR AIAR LA++P VILFDEPTS Sbjct: 127 QKRDRDEVYREARALLERVGVGEKADEYPRQLSGGQQQRVAIARALALRPAVILFDEPTS 186 Query: 183 ALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFE 242 ALDPE+V EVL V+ LA +G T+++VTHE+ FAR+V+ VF+ G++ EQG P QV + Sbjct: 187 ALDPELVGEVLEVLAQLARDGATLVIVTHEVGFAREVADTAVFMDGGVIVEQGPPSQVID 246 Query: 243 NPQSARCKQFMS 254 NP R K F+S Sbjct: 247 NPVHERTKAFLS 258 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: 179 Number of extensions: 5 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: 261 Length adjustment: 24 Effective length of query: 233 Effective length of database: 237 Effective search space: 55221 Effective search space used: 55221 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 24 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