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 PP_4425 PP_4425 putative amino-acid ABC transporter ATP-binding protein y4tH
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__Putida:PP_4425 Length = 255 Score = 249 bits (635), Expect = 5e-71 Identities = 131/251 (52%), Positives = 170/251 (67%), Gaps = 1/251 (0%) Query: 8 LEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQILVS 67 + R++ KRYG+ VL G+ L G+ ++I+G SGSGKST LR + LE +G ILV Sbjct: 2 VSFRSVTKRYGNFTVLDGLELDVSAGEKVAIIGPSGSGKSTLLRVLMTLEGIDEGSILVE 61 Query: 68 GEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGKSK 127 GE L + +NG LV AD++ + +R ++G VFQ FNL+PH + L NV EAP VLG Sbjct: 62 GESLTHMQGRNGKLVPADAKHVRAVRGKIGMVFQGFNLFPHRTALQNVTEAPVHVLGVKP 121 Query: 128 AEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDPE 187 AEA + A LL VG+ K YP+QLSGGQQQR AIAR LAM+PKV+LFDE TSALDPE Sbjct: 122 AEARDRAVQLLEMVGLGAKLDHYPSQLSGGQQQRVAIARALAMRPKVMLFDEVTSALDPE 181 Query: 188 MVQEVLNVIRALAEEGR-TMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENPQS 246 + EVLNVIR L E + TML+VTH+M FAR+ + V F ++G + EQG P Q+FE PQ Sbjct: 182 LCGEVLNVIRRLGSEHKLTMLMVTHQMGFAREFADRVCFFYKGRIHEQGAPGQLFETPQE 241 Query: 247 ARCKQFMSSHR 257 R + F+S+ R Sbjct: 242 ERTRSFLSAVR 252 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: 168 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: 255 Length adjustment: 24 Effective length of query: 233 Effective length of database: 231 Effective search space: 53823 Effective search space used: 53823 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