Align arginine ABC transporter, periplasmic arginine-binding protein ArtJ (characterized)
to candidate BWI76_RS09500 BWI76_RS09500 arginine ABC transporter substrate-binding protein
Query= CharProtDB::CH_002541 (243 letters) >FitnessBrowser__Koxy:BWI76_RS09500 Length = 243 Score = 430 bits (1106), Expect = e-125 Identities = 210/243 (86%), Positives = 226/243 (93%) Query: 1 MKKLVLAALLASFTFGASAAEKINFGVSATYPPFESIGANNEIVGFDIDLAKALCKQMQA 60 MKKLVLAALL+SF FGA+AAEKI+FGVSATYPPFES+ ANN+I GFDIDLA ALCKQMQA Sbjct: 1 MKKLVLAALLSSFAFGAAAAEKISFGVSATYPPFESMDANNQIAGFDIDLANALCKQMQA 60 Query: 61 ECTFTNHAFDSLIPSLKFRKYDAVISGMDITPERSKQVSFTTPYYENSAVVIAKKDTYKT 120 ECTFTNHAFDSLIP+LKF+KYDAVISGMDITP RSKQV+FT PYY NSA+VI+KKD + + Sbjct: 61 ECTFTNHAFDSLIPALKFKKYDAVISGMDITPGRSKQVAFTDPYYANSALVISKKDAFHS 120 Query: 121 FADLKGKRIGMENGTTHQKYIQDQHPEVKTVSYDSYQNAFIDLKNGRIDGVFGDTAVVNE 180 F DLKGKRIGMENGTTHQKY+QD+HPEVKTV+YDSYQNAFIDLKNGRIDGVFGDTAVVNE Sbjct: 121 FDDLKGKRIGMENGTTHQKYLQDKHPEVKTVAYDSYQNAFIDLKNGRIDGVFGDTAVVNE 180 Query: 181 WLKTNPQLGVATEKVTDPQYFGTGLGIAVRPDNKALLEKLNNALAAIKADGTYQKISDQW 240 WLKTNPQLG AT KVTD QYFGTGLGIAVRPDNKALLEKLN AL AIKADGTY KIS QW Sbjct: 181 WLKTNPQLGAATPKVTDAQYFGTGLGIAVRPDNKALLEKLNAALKAIKADGTYDKISKQW 240 Query: 241 FPQ 243 FP+ Sbjct: 241 FPE 243 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: 318 Number of extensions: 5 Number of successful extensions: 1 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: 243 Length adjustment: 23 Effective length of query: 220 Effective length of database: 220 Effective search space: 48400 Effective search space used: 48400 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: 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