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 WP_035130886.1 Q763_RS02520 ABC transporter ATP-binding protein
Query= TCDB::Q9HU32 (257 letters) >NCBI__GCF_000769915.1:WP_035130886.1 Length = 222 Score = 136 bits (342), Expect = 4e-37 Identities = 79/222 (35%), Positives = 129/222 (58%), Gaps = 16/222 (7%) Query: 8 LEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQ---I 64 ++ +N+HK Y L VLKG+ L + G+V+SI+G+SG+GK+T L+ + L+ P + + Sbjct: 2 IQAKNIHKYYDSLHVLKGVDLHIKKGEVVSIVGASGAGKTTLLQILGTLDKPKSEKGTSL 61 Query: 65 LVSGEELRLKKSKNGDLVAADSQQINRLRS-ELGFVFQNFNLWPHMSILDNVIEAPRRVL 123 L+ GE++ K K +++ R+ +LGF+FQ L+P + L+NV P + Sbjct: 62 LIDGEDVLNMKDK----------ALSKFRNLKLGFIFQFHQLFPEFTALENVC-IPAFIA 110 Query: 124 GKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183 GK KAE A+ LL +G++ + + P +LSGG+QQR A+AR L +P VI DEP+ Sbjct: 111 GKQKAETEAEAKKLLEYLGLSHRINHKPGELSGGEQQRVAVARALINKPAVIFADEPSGN 170 Query: 184 LDPEMVQEVLNVIRALAEE-GRTMLLVTHEMSFARQVSSEVV 224 LD + + N+ L +E G+T ++VTH A ++V Sbjct: 171 LDTHSAENLHNLFFKLRDEMGQTFVIVTHNEELANMADRKLV 212 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: 135 Number of extensions: 9 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: 222 Length adjustment: 23 Effective length of query: 234 Effective length of database: 199 Effective search space: 46566 Effective search space used: 46566 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 24 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