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 HSERO_RS21250 HSERO_RS21250 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__HerbieS:HSERO_RS21250 Length = 244 Score = 247 bits (630), Expect = 2e-70 Identities = 130/248 (52%), Positives = 174/248 (70%), Gaps = 11/248 (4%) Query: 6 PALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQIL 65 P + I N+ KR+GD EVLKGISL G+VI+I+G SGSGKST LRCIN LE+ +G I Sbjct: 2 PLIAIDNVKKRFGDNEVLKGISLDVEPGEVIAIIGKSGSGKSTLLRCINGLESIDEGNIS 61 Query: 66 VSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGK 125 V+G +L A ++ LR ++G +FQ FNL+PH+S+ NV+ AP V G Sbjct: 62 VAGAKL-----------GASELELRNLRLKVGMIFQQFNLFPHLSVGRNVMIAPMIVKGV 110 Query: 126 SKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSALD 185 S+AEA++ A+ L KVG+ K +YP QLSGGQQQR AIAR L+M P+ +L DE TSALD Sbjct: 111 SEAEAMKTAKANLEKVGLGHKFDAYPDQLSGGQQQRVAIARALSMSPQALLCDEITSALD 170 Query: 186 PEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENPQ 245 PE+V EVL V+R LA+EG T+L+VTHEM FAR+V + +VF+HQG V E G P+++F NP+ Sbjct: 171 PELVNEVLTVMRGLAKEGMTLLMVTHEMRFAREVCNRLVFMHQGKVHEIGPPEELFGNPK 230 Query: 246 SARCKQFM 253 + +QF+ Sbjct: 231 TPELQQFI 238 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: 170 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: 244 Length adjustment: 24 Effective length of query: 233 Effective length of database: 220 Effective search space: 51260 Effective search space used: 51260 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 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