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 YP_004144758.1 Mesci_5616 ABC transporter
Query= TCDB::Q9HU32 (257 letters) >NCBI__GCF_000185905.1:YP_004144758.1 Length = 270 Score = 317 bits (813), Expect = 1e-91 Identities = 156/250 (62%), Positives = 199/250 (79%) Query: 4 ATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQ 63 A A+ +++LHK++G L VLKG+SL+ARDGDV++I+G SGSGKST LRCIN LENP G Sbjct: 17 AAEAIHVQDLHKKFGALHVLKGVSLSARDGDVVAIIGGSGSGKSTLLRCINCLENPTSGV 76 Query: 64 ILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVL 123 I V+GEE+RLK NG + AD +QI R+RS LG VFQ+FNLW HM++++NVIE P VL Sbjct: 77 IRVNGEEIRLKPDGNGSTLPADRKQIERVRSRLGMVFQSFNLWTHMTLIENVIEVPVHVL 136 Query: 124 GKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183 G + AI AE LLA+VG+ +KRH YPA LSGGQQQR AIAR LA+QP+V+LFDEPTS+ Sbjct: 137 GVKREMAIIEAEKLLARVGLLEKRHVYPAFLSGGQQQRGAIARALAVQPRVMLFDEPTSS 196 Query: 184 LDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFEN 243 LDPE++ EVL VI LA EGRTM+LVTHEM FAR+V++ VVFLH+G VEE+G+P +F + Sbjct: 197 LDPELIGEVLGVIGDLAREGRTMILVTHEMKFAREVATRVVFLHEGRVEEEGSPDAIFGS 256 Query: 244 PQSARCKQFM 253 P+S R +QF+ Sbjct: 257 PKSERLQQFI 266 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: 198 Number of extensions: 4 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: 270 Length adjustment: 25 Effective length of query: 232 Effective length of database: 245 Effective search space: 56840 Effective search space used: 56840 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 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