Align lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized)
to candidate WP_046158297.1 VL52_RS17825 ABC transporter substrate-binding protein
Query= CharProtDB::CH_003045 (260 letters) >NCBI__GCF_000971335.1:WP_046158297.1 Length = 254 Score = 221 bits (563), Expect = 1e-62 Identities = 114/259 (44%), Positives = 158/259 (61%), Gaps = 6/259 (2%) Query: 1 MKKTVLALSLLIGLGATAASYAALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMC 60 MKK ++A + + A AS +A +T+RIG D Y PFS + A G+ GFDID+ N +C Sbjct: 1 MKKALIASAGI----ALLASLSAQAETLRIGVDLNYPPFSKQGADGKPQGFDIDIANSLC 56 Query: 61 KRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAK 120 M+V C V D+D LIP+L A K DAIISS+ IT +RQ+ + FS K Y SR++A Sbjct: 57 AAMKVTCQIVPQDWDGLIPALNANKFDAIISSMQITPERQKAVDFSHKYYNIASRMVAKD 116 Query: 121 GSPIQPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAA 180 G+ + SLKGK +GVL+ STQE +A DNW G +V+YA + DL +GR+DA Sbjct: 117 GTKVDAA--SLKGKKIGVLRASTQEKFAKDNWGKNGAAIVSYAKSPESFLDLKSGRVDAV 174 Query: 181 LQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELR 240 D + FLK K YAF GP+ D KYFG G G+ ++K + L +KA+ ++R Sbjct: 175 FVDSAVGEQEFLKTAQAKGYAFVGPNYSDVKYFGPGCGIAVKKGNKALVERLNKAIDQIR 234 Query: 241 QDGTYDKMAKKYFDFNVYG 259 +DG Y K+ KYF F++YG Sbjct: 235 KDGAYKKVQDKYFSFDIYG 253 Lambda K H 0.315 0.132 0.374 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: 218 Number of extensions: 8 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: 260 Length of database: 254 Length adjustment: 24 Effective length of query: 236 Effective length of database: 230 Effective search space: 54280 Effective search space used: 54280 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