Align arginine ABC transporter, periplasmic arginine-binding protein ArtJ (characterized)
to candidate 5210738 Shew_3166 extracellular solute-binding protein (RefSeq)
Query= CharProtDB::CH_002541 (243 letters) >FitnessBrowser__PV4:5210738 Length = 242 Score = 122 bits (307), Expect = 5e-33 Identities = 80/245 (32%), Positives = 126/245 (51%), Gaps = 21/245 (8%) Query: 2 KKLVLAALLASFTFGASAAEK--INFGVSATYPPFESIG--ANNEIVGFDIDLAKALCKQ 57 K ++LA A E+ + G +A +PPFE +G + ++++GFDIDLA+ + + Sbjct: 3 KSILLAGFTALLLLSGCGKEQDYLVVGTNAAFPPFEYVGGVSGDQVMGFDIDLARKVAED 62 Query: 58 MQAECTFTNHAFDSLIPSLKFRKYDAVISGMDITPERSKQVSFTTPYYENSAVVIAKK-- 115 N FDSLI +L K D + SGM ITPER V F+ PYYE + VV+ K Sbjct: 63 AGKTLKVENMKFDSLIVALNAGKIDMIASGMTITPERQASVDFSEPYYEATQVVLVNKQD 122 Query: 116 DTYKTFADLKGKRIGMENGTT----HQKYIQDQHPEVKTVSYDSYQNAFIDLKNGRIDGV 171 D+ + ADL GK ++ G+T +KY Q ++++ A ++LKNG++D V Sbjct: 123 DSIHSLADLTGKHFAVQLGSTADMMAKKYTQ------SVTAFNTGFEAIMELKNGKVDLV 176 Query: 172 FGDTAVVNEWLKTNPQLGVATEKVTDPQYFGTGLGIAVRPDNKALLEKLNNALAAIKADG 231 D+ +L NP+L + + P+++ G AV LL +N LA +K +G Sbjct: 177 LFDSEPAANYLAKNPELKLISLDF-PPEFY----GFAVAKSQPELLASINKTLATMKQNG 231 Query: 232 TYQKI 236 Y + Sbjct: 232 EYDAL 236 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: 162 Number of extensions: 7 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: 242 Length adjustment: 23 Effective length of query: 220 Effective length of database: 219 Effective search space: 48180 Effective search space used: 48180 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