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_047005877.1 AAW01_RS03230 ABC transporter ATP-binding protein
Query= TCDB::Q9HU32 (257 letters) >NCBI__GCF_001010925.1:WP_047005877.1 Length = 226 Score = 137 bits (346), Expect = 1e-37 Identities = 87/237 (36%), Positives = 137/237 (57%), Gaps = 16/237 (6%) Query: 1 MAEATPALEIRNLHKRY--GD--LEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLL 56 M+ A + +RNL + + GD ++VL+G+ L G+++++LG SGSGKST L+ + LL Sbjct: 1 MSNAEAVVSLRNLTRSFQQGDVRIDVLRGVDLDVGPGEIVALLGQSGSGKSTMLQAVGLL 60 Query: 57 ENPHQGQILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVI 116 E G I ++G+E L AA+ + R LGFV+Q +L P + +NV+ Sbjct: 61 EGGFGGSIRIAGKEA-------SQLDAAERTSLRR--EHLGFVYQFHHLLPDFTAQENVV 111 Query: 117 EAPRRVLGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVIL 176 P+ +LG +AEA A+ LL +G+ + P++LSGG+QQR A+AR LA +P+++L Sbjct: 112 -LPQLLLGTKRAEAELRAQELLGSLGLEHRLTHRPSKLSGGEQQRVAVARALANKPQLVL 170 Query: 177 FDEPTSALDPEMVQEVLNVIRALAE-EGRTMLLVTHEMSFARQVSSEVVFLHQGLVE 232 DEPT LD + + VL+ L +G L+ TH A ++ VV LH G++E Sbjct: 171 ADEPTGNLDEKTSERVLSEFLELVRGQGSAALVATHNERLAARM-DRVVRLHDGVIE 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: 115 Number of extensions: 5 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: 226 Length adjustment: 23 Effective length of query: 234 Effective length of database: 203 Effective search space: 47502 Effective search space used: 47502 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