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_012411414.1 NPUN_RS25940 ABC transporter ATP-binding protein
Query= TCDB::Q9HU32 (257 letters) >NCBI__GCF_000020025.1:WP_012411414.1 Length = 254 Score = 142 bits (359), Expect = 5e-39 Identities = 88/238 (36%), Positives = 129/238 (54%), Gaps = 16/238 (6%) Query: 8 LEIRNLHKRYG----DLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQ 63 + + N+ K YG ++ L ++L G+ +I+G SGSGKST + I L+ P G Sbjct: 22 IRLENIFKIYGSGETEVRALNDVNLIVEQGEYCAIMGPSGSGKSTAMNIIGCLDRPTTGH 81 Query: 64 ILVSGEELRLKKSKNGDLVAADSQQINRLRSE-LGFVFQNFNLWPHMSILDNVIEAPRRV 122 + N D+ D + + +R++ LGFVFQ F+L P ++ L+NVI P Sbjct: 82 YYLD----------NLDVAQMDDRSLAHIRNKKLGFVFQQFHLLPQLTALENVI-LPMLY 130 Query: 123 LGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTS 182 G + E + A L +VG+A++ ++ P QLSGGQQQR AIAR + +P V+L DEPT Sbjct: 131 AGVNPKERSDRAIVALTRVGLANRLNNKPTQLSGGQQQRVAIARAIVNRPVVLLADEPTG 190 Query: 183 ALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQV 240 ALD QEVL++ L G T+++VTHE ARQ V F +V TP + Sbjct: 191 ALDSRTTQEVLDIFSELNASGITVVMVTHEPEVARQTQRIVWFRDGQVVHSNLTPSDL 248 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: 142 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: 254 Length adjustment: 24 Effective length of query: 233 Effective length of database: 230 Effective search space: 53590 Effective search space used: 53590 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 Apr 09 2024. 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