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_110206230.1 DNK54_RS07055 ABC transporter ATP-binding protein
Query= TCDB::Q9HU32 (257 letters) >NCBI__GCF_003194585.1:WP_110206230.1 Length = 231 Score = 152 bits (384), Expect = 6e-42 Identities = 91/237 (38%), Positives = 135/237 (56%), Gaps = 17/237 (7%) Query: 4 ATPALEIRNLHKRY----GDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENP 59 +TP LE++ + K Y G +E ++GI G+ ++++G SGSGKST + + L+ P Sbjct: 2 STPVLELQGVRKTYSTGAGAVEAVRGIDAVVVAGEYVAVVGPSGSGKSTLMHILGCLDVP 61 Query: 60 HQGQILVSGEELRLKKSKNGDLVAADSQQINRLRS-ELGFVFQNFNLWPHMSILDNVIEA 118 G+ LV G+ D+ A D Q+ +R+ E+GFVFQ F+L P ++ L NV E Sbjct: 62 TSGRQLVRGQ----------DVAAMDEAQLAAVRNREIGFVFQQFHLLPGLTALRNV-EL 110 Query: 119 PRRVLGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFD 178 P G + E A L +VG+ D+ P +LSGGQQQR AIAR L P ++L D Sbjct: 111 PLIYAGVTALERRRRATVALTRVGLGDRADHRPGELSGGQQQRVAIARALVTDPALVLAD 170 Query: 179 EPTSALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQG 235 EPT LD +VL + R L ++GRT++L+THE A + + V+ L GL+E+ G Sbjct: 171 EPTGNLDSRATADVLALFRELHDQGRTIVLITHEQEVAAE-ADRVLTLRDGLLEDAG 226 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: 111 Number of extensions: 7 Number of successful extensions: 3 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: 231 Length adjustment: 24 Effective length of query: 233 Effective length of database: 207 Effective search space: 48231 Effective search space used: 48231 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