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 BWI76_RS07590 BWI76_RS07590 glutamate ABC transporter ATP-binding protein
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__Koxy:BWI76_RS07590 Length = 253 Score = 265 bits (677), Expect = 7e-76 Identities = 138/253 (54%), Positives = 183/253 (72%), Gaps = 3/253 (1%) Query: 5 TPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQI 64 T A+ ++N+ K++ ++EVL+ I+LT G V+SILGSSGSGKST LRC+N LE P +G+I Sbjct: 4 TTAVSVKNVSKQFDNVEVLRDINLTVEKGTVVSILGSSGSGKSTLLRCMNWLEQPDRGEI 63 Query: 65 LVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLG 124 +SG+ L + + NG A +Q++++R +G VFQ+FNLWPH+++ NV EA V G Sbjct: 64 RISGQRLGIDEH-NGR--AMSHRQLSKIRERVGMVFQSFNLWPHLTVQQNVSEALLHVKG 120 Query: 125 KSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSAL 184 + EA IA L KVG+A K YP LSGGQ+QR AIAR+LAM P+VILFDEPTSAL Sbjct: 121 MKRDEAKAIAMQQLEKVGMAHKADVYPITLSGGQKQRVAIARSLAMSPEVILFDEPTSAL 180 Query: 185 DPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENP 244 DPE+V EVL V++ALA EG TM++VTHEM FARQVS EVVFL +GL+ E+ P++ F NP Sbjct: 181 DPELVNEVLGVMKALAAEGYTMVVVTHEMDFARQVSDEVVFLEKGLLIEKAPPEKFFSNP 240 Query: 245 QSARCKQFMSSHR 257 S R +QF+ R Sbjct: 241 DSERVRQFLQGSR 253 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: 165 Number of extensions: 3 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: 253 Length adjustment: 24 Effective length of query: 233 Effective length of database: 229 Effective search space: 53357 Effective search space used: 53357 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