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 350222 BT0694 ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__Btheta:350222 Length = 224 Score = 143 bits (361), Expect = 3e-39 Identities = 83/218 (38%), Positives = 129/218 (59%), Gaps = 17/218 (7%) Query: 8 LEIRNLHKRYGDLEV----LKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQ 63 ++I N+ K + EV L ++L ++G+ ++I+G SG GKST L + LL+NP +G Sbjct: 2 IQIENISKVFRTTEVETVALNHVNLEVKEGEFVAIMGPSGCGKSTLLNILGLLDNPTEGS 61 Query: 64 ILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVL 123 + GEE+ K K ++ + +LGFVFQ+FNL +++ +NV E P L Sbjct: 62 YRLLGEEVAGLKEK---------ERTGVRKGKLGFVFQSFNLIDELNVFENV-ELPLTYL 111 Query: 124 GKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183 G +E + E +L ++ I+ + +P QLSGGQQQR AIAR + PK+IL DEPT Sbjct: 112 GIKSSERRRMVEDILKRMNISHRAKHFPQQLSGGQQQRVAIARAVVTNPKLILADEPTGN 171 Query: 184 LDPEMVQEVLNVIRALAEEGRTMLLVT---HEMSFARQ 218 LD + EV+N++ L +EG T+++VT H+ SFA + Sbjct: 172 LDSKNGAEVMNLLTELNKEGTTIIMVTHSQHDASFAHR 209 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: 137 Number of extensions: 7 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: 224 Length adjustment: 23 Effective length of query: 234 Effective length of database: 201 Effective search space: 47034 Effective search space used: 47034 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