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_053938863.1 WG78_RS16125 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q9HU32 (257 letters) >NCBI__GCF_001294205.1:WP_053938863.1 Length = 246 Score = 244 bits (622), Expect = 2e-69 Identities = 130/247 (52%), Positives = 171/247 (69%), Gaps = 12/247 (4%) Query: 8 LEIRNLHKRYG-DLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQILV 66 + ++K YG D VLK ISL + G+V+ + G SGSGKST +R IN LE + G+I V Sbjct: 2 IRFNQVNKWYGRDHHVLKNISLEVKQGEVVVVCGPSGSGKSTLIRTINQLEPVNDGEIWV 61 Query: 67 SGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGKS 126 G ++ ++ INRLR E+GFVFQ+FNL+PH+S+L N+ AP +V S Sbjct: 62 DGVQVNHPRTN-----------INRLREEVGFVFQHFNLYPHLSVLQNITLAPVKVRKMS 110 Query: 127 KAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDP 186 +A+A + LL +VG+++KR +YP+QLSGGQQQR AIAR LAMQPKV+LFDEPTSALDP Sbjct: 111 QADADQRGMELLERVGLSNKRDAYPSQLSGGQQQRVAIARGLAMQPKVMLFDEPTSALDP 170 Query: 187 EMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENPQS 246 EM+ EVL V++ LAE G TM++VTHEM FAR+V+ VVFL G + EQ P Q F NPQ Sbjct: 171 EMIGEVLKVMQNLAESGMTMMVVTHEMGFAREVADRVVFLDHGEILEQAAPAQFFNNPQC 230 Query: 247 ARCKQFM 253 R +QF+ Sbjct: 231 DRAQQFL 237 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: 178 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: 246 Length adjustment: 24 Effective length of query: 233 Effective length of database: 222 Effective search space: 51726 Effective search space used: 51726 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: 46 (22.3 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