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 6938761 Sama_2864 ABC transporter related (RefSeq)
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__SB2B:6938761 Length = 230 Score = 138 bits (347), Expect = 1e-37 Identities = 80/221 (36%), Positives = 130/221 (58%), Gaps = 16/221 (7%) Query: 8 LEIRNLHKRYG----DLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQ 63 L ++N++K + + L+ +L +G+ +++ G SGSGK+TFL LLEN G+ Sbjct: 2 LTMKNINKLFRTDLVETHALRDFNLEVAEGEFVAVTGPSGSGKTTFLNIAGLLENASGGE 61 Query: 64 ILVSGEELRLKKSKNGDLVAADSQQINRLRSE-LGFVFQNFNLWPHMSILDNVIEAPRRV 122 + GE + + D AA R+R++ +GF+FQ FNL P +++ +NV E P R Sbjct: 62 YWLDGENV----ANLSDSAAA------RVRNQKIGFIFQGFNLIPDLNLAENV-ELPLRY 110 Query: 123 LGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTS 182 G +E E L++VG+A ++ P+QLSGGQQQR AIAR LA +P+ +L DEPT Sbjct: 111 RGFGSSERKRRVEQALSQVGLAARQKHLPSQLSGGQQQRVAIARALAGEPRFLLADEPTG 170 Query: 183 ALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEV 223 LD M ++V+ ++ + +G T+++VTH+ AR+ + Sbjct: 171 NLDSLMARQVMELLEDINRQGTTIIMVTHDGELARRAERNI 211 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: 131 Number of extensions: 6 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: 230 Length adjustment: 23 Effective length of query: 234 Effective length of database: 207 Effective search space: 48438 Effective search space used: 48438 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