Align arginine ABC transporter, periplasmic arginine-binding protein ArtJ (characterized)
to candidate RR42_RS36985 RR42_RS36985 amino acid ABC transporter substrate-binding protein
Query= CharProtDB::CH_002541 (243 letters) >FitnessBrowser__Cup4G11:RR42_RS36985 Length = 270 Score = 102 bits (253), Expect = 1e-26 Identities = 67/223 (30%), Positives = 111/223 (49%), Gaps = 9/223 (4%) Query: 23 INFGVSATYPPFESIGANNEI-VGFDIDLAKALCKQMQAECTFTNHAFDSLIPSLKFRKY 81 + GV PPF + A + VG D+D A + K++ + F + I L +K Sbjct: 34 LRVGVFDANPPFGFVEAGSITPVGLDVDYAAEIAKRLGVKPEFRATNPANRIALLASQKA 93 Query: 82 DAVISGMDITPERSKQVSFTTPYYENSAVVIAKKDTYKTFADLKGKRIGMENGTTHQKYI 141 D V + IT ER +Q+ F+TPY+ + IA+K K DLK R+G++ GTT + + Sbjct: 94 DIVAANFTITDERRQQIGFSTPYFASGLQFIARKGALKQADDLKAWRLGVDKGTTQETTL 153 Query: 142 QDQHPEVKTVSYDSYQNAFIDLKNGRIDGVFGDTAVVNEWLKTNP---QLGVATEKVTDP 198 + ++P+ + ++YD A L++G I D A + L T P Q +++ +T Sbjct: 154 RQKYPDARVIAYDDSPLALSALRSGAIQAFAQDGAKLGALLATLPNKDQFEISSFTLT-R 212 Query: 199 QYFGTGLGIAVRPDNKALLEKLNNALAAIKADGTYQKISDQWF 241 +Y G G V L +++ LA ++ DGT +I D+WF Sbjct: 213 EYMGVG----VPKGEDRLTAEIDRILAGLEKDGTAARIYDKWF 251 Lambda K H 0.317 0.133 0.384 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: 164 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: 243 Length of database: 270 Length adjustment: 24 Effective length of query: 219 Effective length of database: 246 Effective search space: 53874 Effective search space used: 53874 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 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