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 SMc02260 SMc02260 ABC transporter ATP-binding protein
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__Smeli:SMc02260 Length = 284 Score = 330 bits (845), Expect = 3e-95 Identities = 164/255 (64%), Positives = 206/255 (80%) Query: 1 MAEATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPH 60 M +A A+ + +LHKR+G LEVLKG+SL+AR GDVI+I+G SGSGKST LRCIN+LE P Sbjct: 28 MTDAAQAIAVTDLHKRFGPLEVLKGVSLSARQGDVIAIIGGSGSGKSTLLRCINMLELPS 87 Query: 61 QGQILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPR 120 GQI V GEE+R+K +G L+ AD +Q+ R+R++LG VFQ+FNLW HM+IL NVIEAP Sbjct: 88 AGQISVHGEEIRMKPDGHGGLMPADRKQVQRIRTQLGMVFQSFNLWQHMTILQNVIEAPV 147 Query: 121 RVLGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEP 180 VLGK+KAEA+E AE LL +VG+ +KR +YPA LSGGQQQRAAIAR LA+QP V+LFDEP Sbjct: 148 HVLGKTKAEAVETAEALLRRVGLYEKRDAYPAFLSGGQQQRAAIARALAIQPLVMLFDEP 207 Query: 181 TSALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQV 240 TSALDPE+V EVL+VI LA E RTM+LVTHEM FAR V++ +VFLH G++EEQG P+ + Sbjct: 208 TSALDPELVGEVLSVIGDLAREERTMVLVTHEMKFARDVANHIVFLHNGVIEEQGPPEAI 267 Query: 241 FENPQSARCKQFMSS 255 F P+S R K+F+SS Sbjct: 268 FGAPKSERLKKFISS 282 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: 202 Number of extensions: 3 Number of successful extensions: 1 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: 284 Length adjustment: 25 Effective length of query: 232 Effective length of database: 259 Effective search space: 60088 Effective search space used: 60088 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