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 Ac3H11_3327 Glutamine transport ATP-binding protein GlnQ (TC 3.A.1.3.2)
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3327 Length = 249 Score = 238 bits (608), Expect = 7e-68 Identities = 130/251 (51%), Positives = 164/251 (65%), Gaps = 11/251 (4%) Query: 3 EATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQG 62 +ATP + + + K +G +VLK +S T G+V I+G+SGSGKST LR IN LE G Sbjct: 5 QATPFIVVDRVCKSFGAHQVLKDVSTTFNTGEVTVIIGASGSGKSTLLRAINRLEPHDSG 64 Query: 63 QILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRV 122 I + GE + GD D + + RSE+G VFQ FNL+ HMS+LDNV APRR+ Sbjct: 65 TITIGGEPV-------GD----DQHLLQKQRSEVGMVFQQFNLFGHMSVLDNVTLAPRRI 113 Query: 123 LGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTS 182 + +A A LL +VG+ D H YP QLSGGQQQR AIAR LAMQPKV+LFDEPTS Sbjct: 114 RHTPRTQANAQALALLTRVGMQDHAHKYPWQLSGGQQQRVAIARALAMQPKVMLFDEPTS 173 Query: 183 ALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFE 242 ALDPEMVQEVL+V+R LA G TM++VTHEM FAR+VS V+F QG + P + F Sbjct: 174 ALDPEMVQEVLDVMRELARGGMTMIVVTHEMGFAREVSDRVMFFDQGRIAHDAPPAEFFN 233 Query: 243 NPQSARCKQFM 253 NP + R + F+ Sbjct: 234 NPANDRIRAFI 244 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: 170 Number of extensions: 4 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: 249 Length adjustment: 24 Effective length of query: 233 Effective length of database: 225 Effective search space: 52425 Effective search space used: 52425 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