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 YP_004141922.1 Mesci_2738 ABC transporter
Query= TCDB::Q9HU32 (257 letters) >NCBI__GCF_000185905.1:YP_004141922.1 Length = 252 Score = 244 bits (622), Expect = 2e-69 Identities = 127/250 (50%), Positives = 175/250 (70%), Gaps = 11/250 (4%) Query: 5 TPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQI 64 T ++ R ++K +G L VLK I+L+ +V+ + G SGSGKST +RC+N LE G + Sbjct: 9 TGMIDFRGVNKWFGSLNVLKDITLSVEPREVVVVCGPSGSGKSTLIRCVNGLEAIKNGDL 68 Query: 65 LVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLG 124 +V G+ L GD + + +LR+E+GFVFQ+FNL+PH + L+NV AP V Sbjct: 69 VVDGQRL-------GD----PATNMTQLRTEIGFVFQSFNLYPHKTALENVTLAPIHVRK 117 Query: 125 KSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSAL 184 +AEA + LLAKVG+ADK ++YPAQLSGGQQQR AIAR L M+PK++LFDEPTSAL Sbjct: 118 IPRAEAEKAGRELLAKVGLADKVNAYPAQLSGGQQQRVAIARCLGMRPKIMLFDEPTSAL 177 Query: 185 DPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENP 244 DPEM+ EVL+V+ A+AEEG TM++VTHEM FAR+V+ VVF+ G + E GTP + F +P Sbjct: 178 DPEMISEVLDVMVAVAEEGMTMMVVTHEMGFARKVAQRVVFMDAGAIVESGTPDEFFSHP 237 Query: 245 QSARCKQFMS 254 ++ R + F+S Sbjct: 238 KTDRSRAFLS 247 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: 167 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: 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 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