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 3606891 Dshi_0321 ABC transporter related (RefSeq)
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__Dino:3606891 Length = 258 Score = 237 bits (604), Expect = 2e-67 Identities = 127/248 (51%), Positives = 167/248 (67%), Gaps = 11/248 (4%) Query: 7 ALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQILV 66 A+EI ++K YG VL+ I+LT G+ I I G SGSGKST +RCIN LE G I V Sbjct: 17 AIEIDKMNKWYGQFHVLRDINLTVYRGERIVICGPSGSGKSTLIRCINALEEHQAGSITV 76 Query: 67 SGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGKS 126 +G L+++D + I+ +RSE+G FQ+FNL+PH++IL+N AP V Sbjct: 77 -----------DGTLLSSDLKNIDTIRSEVGMCFQHFNLFPHLTILENCTLAPIWVRKTP 125 Query: 127 KAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDP 186 K EA A L KV I D+ + YP QLSGGQQQR AIAR+L M+P+++LFDEPTSALDP Sbjct: 126 KKEAEATAMHFLEKVKIPDQANKYPGQLSGGQQQRVAIARSLCMRPRIMLFDEPTSALDP 185 Query: 187 EMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENPQS 246 EM++EVL+ + LAEEG TM+ VTHEM FARQV++ V+F+ G + EQ P++ F NPQS Sbjct: 186 EMIKEVLDTMIELAEEGMTMICVTHEMGFARQVANRVIFMDAGQIVEQNEPEEFFGNPQS 245 Query: 247 ARCKQFMS 254 R K F+S Sbjct: 246 DRTKLFLS 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: 151 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