Align arginine ABC transporter, periplasmic arginine-binding protein ArtJ (characterized)
to candidate RR42_RS31745 RR42_RS31745 ABC transporter permease
Query= CharProtDB::CH_002541 (243 letters) >FitnessBrowser__Cup4G11:RR42_RS31745 Length = 249 Score = 132 bits (333), Expect = 5e-36 Identities = 79/245 (32%), Positives = 125/245 (51%), Gaps = 11/245 (4%) Query: 2 KKLVLAALLASFTFGASAAEK---INFGVSATYPPFESIGANNEIVGFDIDLAKALCKQM 58 K L++ + S G + A+ + AT+PP E + N + GFD++L +AL K M Sbjct: 6 KCLLIGLMGLSLAAGLARAQDNAVLRVATDATFPPMEFV-ENGKRTGFDVELVEALAKTM 64 Query: 59 QAECTFTNHAFDSLIPSLKFRKYDAVISGMDITPERSKQVSFTTPYYENSAVVIAK--KD 116 +T+ F LIP L R++D +SG+ IT ER K V FT PYY V + K Sbjct: 65 GKRVEWTDIDFKGLIPGLISRRFDMAVSGIYITEERRKVVDFTDPYYTGGLVALVKSGNT 124 Query: 117 TYKTFADLKGKRIGMENGTTHQKYIQDQHPEVKTVSYDSYQNAFIDLKNGRIDGVFGDTA 176 T ADL GK++ ++ GT ++++ +P+V+ V + Q F ++ GR D Sbjct: 125 AINTPADLNGKKVSVQVGTKSVNFLRENYPQVQRVEVEKNQEMFNLVEIGRADAAVTGKP 184 Query: 177 VVNEWLKTNPQLGVATEKVTDPQYFGTGLGIAVRPDNKALLEKLNNALAAIKADGTYQKI 236 +++K + V + +T +Y G+AVR D L +N AL +KADGTY ++ Sbjct: 185 AAMQYVKARGGMRVVEKALTTEEY-----GMAVRKDTPELTRAVNAALTKLKADGTYAQL 239 Query: 237 SDQWF 241 +WF Sbjct: 240 VQKWF 244 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: 150 Number of extensions: 14 Number of successful extensions: 3 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: 249 Length adjustment: 24 Effective length of query: 219 Effective length of database: 225 Effective search space: 49275 Effective search space used: 49275 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