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 6937163 Sama_1333 lipoprotein releasing system ATP-binding protein LolD (RefSeq)
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__SB2B:6937163 Length = 229 Score = 135 bits (340), Expect = 7e-37 Identities = 86/221 (38%), Positives = 129/221 (58%), Gaps = 15/221 (6%) Query: 8 LEIRNLHKRY--GDLE--VLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQ 63 L++ N+ K Y G LE VL G+ L+ G+ ++I+G SGSGKST L + L+ P G+ Sbjct: 6 LKVENVSKTYREGKLETQVLCGVDLSVYRGEQLAIVGGSGSGKSTLLHIMGSLDKPTSGK 65 Query: 64 ILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVL 123 +L+ GE+L L AA QI + LGF++Q +L P S L+NV P R+ Sbjct: 66 VLLEGEDLY-------SLSAARQAQIRN--ASLGFIYQFHHLLPEFSALENVA-MPARIA 115 Query: 124 GKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183 G K A AE LL +VG++ + P++LSGG++QR AIAR L QP+++L DEPT Sbjct: 116 GVDKKTAFGRAEALLERVGLSHRLSHAPSELSGGERQRVAIARALINQPRLVLADEPTGN 175 Query: 184 LDPEMVQEVLNVIRALAEE-GRTMLLVTHEMSFARQVSSEV 223 LD + V +IR LA + G ++VTH+ + A ++ ++ Sbjct: 176 LDAASGEAVYALIRELAAQLGTAFVVVTHDNALAARMDRQL 216 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: 97 Number of extensions: 4 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: 229 Length adjustment: 23 Effective length of query: 234 Effective length of database: 206 Effective search space: 48204 Effective search space used: 48204 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