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 Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 152 bits (385), Expect = 7e-42 Identities = 89/253 (35%), Positives = 147/253 (58%), Gaps = 19/253 (7%) Query: 7 ALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQILV 66 ++EIRN+ KR+G+ L +SL+ G+++++LG SG GK+T LR I +E +GQ++ Sbjct: 2 SIEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMF 61 Query: 67 SGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGKS 126 G E + ++ ++GFVFQ++ L+ HM++ +NV R K Sbjct: 62 EGSE---------------ATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKE 106 Query: 127 KAEAIEIAE---GLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183 + EI + LL+ V + YP QLSGGQ+QR A+AR LA++PKV+L DEP A Sbjct: 107 RPCESEIRKRVMDLLSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGA 166 Query: 184 LDPEMVQEVLNVIRALAEEGR-TMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFE 242 LD ++ +E+ +R L +E + + VTH+ A +V+ VV +++G +E+ G+P +V+ Sbjct: 167 LDTKVRKELRRWLRRLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYS 226 Query: 243 NPQSARCKQFMSS 255 NP S QF+ + Sbjct: 227 NPASPFVYQFLGN 239 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: 218 Number of extensions: 11 Number of successful extensions: 4 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: 360 Length adjustment: 27 Effective length of query: 230 Effective length of database: 333 Effective search space: 76590 Effective search space used: 76590 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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