Align AotJ aka PA0888, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate WP_046158297.1 VL52_RS17825 ABC transporter substrate-binding protein
Query= TCDB::O50181 (259 letters) >NCBI__GCF_000971335.1:WP_046158297.1 Length = 254 Score = 250 bits (638), Expect = 2e-71 Identities = 128/255 (50%), Positives = 173/255 (67%), Gaps = 3/255 (1%) Query: 3 KLALLGALALSVLSLPTFAADKPVRIGIEAAYPPFSLKTPDGQLAGFDVDIGNALCEEMK 62 K AL+ + +++L+ + A+ +RIG++ YPPFS + DG+ GFD+DI N+LC MK Sbjct: 2 KKALIASAGIALLASLSAQAET-LRIGVDLNYPPFSKQGADGKPQGFDIDIANSLCAAMK 60 Query: 63 VQCKWVEQEFDGLIPALKVRKIDAILSSMTITDERKRSVDFTNKYYNTPARFVMKEGASL 122 V C+ V Q++DGLIPAL K DAI+SSM IT ER+++VDF++KYYN +R V K+G + Sbjct: 61 VTCQIVPQDWDGLIPALNANKFDAIISSMQITPERQKAVDFSHKYYNIASRMVAKDGTKV 120 Query: 123 NDPKADLKGKKAGVLRGSTADRYASAELTPAGVEVVRYNSQQEANMDLVAGRLDAVVADS 182 + A LKGKK GVLR ST +++A G +V Y E+ +DL +GR+DAV DS Sbjct: 121 D--AASLKGKKIGVLRASTQEKFAKDNWGKNGAAIVSYAKSPESFLDLKSGRVDAVFVDS 178 Query: 183 VNLEDGFLKTDAGKGYAFVGPQLTDAKYFGEGVGIAVRKGDSELAGKFNAAIDALRANGK 242 E FLKT KGYAFVGP +D KYFG G GIAV+KG+ L + N AID +R +G Sbjct: 179 AVGEQEFLKTAQAKGYAFVGPNYSDVKYFGPGCGIAVKKGNKALVERLNKAIDQIRKDGA 238 Query: 243 YKQIQDKYFSFDVYG 257 YK++QDKYFSFD+YG Sbjct: 239 YKKVQDKYFSFDIYG 253 Lambda K H 0.316 0.135 0.381 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: 224 Number of extensions: 6 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: 259 Length of database: 254 Length adjustment: 24 Effective length of query: 235 Effective length of database: 230 Effective search space: 54050 Effective search space used: 54050 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 (21.6 bits) S2: 47 (22.7 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