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 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__MR1:202699 Length = 376 Score = 144 bits (362), Expect = 3e-39 Identities = 87/253 (34%), Positives = 137/253 (54%), Gaps = 19/253 (7%) Query: 7 ALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQILV 66 ++ + N+ K++G + L ++L ++G++I +LG SGSGK+T LR I LE G I Sbjct: 2 SIRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHIHF 61 Query: 67 SGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGKS 126 D Q++ +GFVFQN+ L+ HM++ DNV + K Sbjct: 62 GNR---------------DVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQ 106 Query: 127 KAEAIEIAEG---LLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183 + A EI + LL V + YP QLSGGQ+QR A+AR LA QP+V+L DEP A Sbjct: 107 RPSAAEIQKRVSHLLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGA 166 Query: 184 LDPEMVQEVLNVIRALAEEGR-TMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFE 242 LD ++ +E+ +R+L +E + T + VTH+ A ++S VV + G +E+ TP +++ Sbjct: 167 LDAKVRKELRRWLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYA 226 Query: 243 NPQSARCKQFMSS 255 P S F+ + Sbjct: 227 QPNSRFVFDFLGN 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: 193 Number of extensions: 7 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: 376 Length adjustment: 27 Effective length of query: 230 Effective length of database: 349 Effective search space: 80270 Effective search space used: 80270 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 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