Align arginine ABC transporter, periplasmic arginine-binding protein ArtJ (characterized)
to candidate 200227 SO1044 amino acid ABC transporter, periplasmic amino acid-binding protein (NCBI ptt file)
Query= CharProtDB::CH_002541 (243 letters) >FitnessBrowser__MR1:200227 Length = 244 Score = 122 bits (306), Expect = 7e-33 Identities = 85/247 (34%), Positives = 127/247 (51%), Gaps = 23/247 (9%) Query: 2 KKLVLAALLASFTF---GASAAEKINF-GVSATYPPFESIG--ANNEIVGFDIDLAKALC 55 K ++L L + T G +E + G +A +PPFE +G + +EI GFDI+LAK + Sbjct: 3 KSMLLGGLTLTATLLLAGCGKSEDVLVVGTNAAFPPFEYVGGQSGDEIKGFDIELAKQIA 62 Query: 56 KQMQAECTFTNHAFDSLIPSLKFRKYDAVISGMDITPERSKQVSFTTPYYENSAVVIAKK 115 K N FDSLI +L K D + SGM ITPER V+F+ PYYE + V++ K Sbjct: 63 KDAGKTLKVENMKFDSLIVALNSGKIDFIASGMTITPERQASVNFSEPYYEATQVLLVNK 122 Query: 116 D--TYKTFADLKGKRIGMENGTT----HQKYIQDQHPEVKTVSYDSYQNAFIDLKNGRID 169 D + T D+K K ++ G+T +KY Q K ++++ A ++LKNG++D Sbjct: 123 DNESIHTLDDIKDKHFAVQLGSTADMMSKKYTQ------KVTAFNTGFEAIMELKNGKVD 176 Query: 170 GVFGDTAVVNEWLKTNPQLGVATEKVTDPQYFGTGLGIAVRPDNKALLEKLNNALAAIKA 229 V D+ +L NP L + K+ P F G AV LL +N+ L +K Sbjct: 177 LVLFDSEPAANYLAKNPDLKLI--KLDFPPEF---YGFAVSKQQPELLNSINHTLKNLKE 231 Query: 230 DGTYQKI 236 +G YQ + Sbjct: 232 NGQYQAL 238 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: 153 Number of extensions: 7 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: 244 Length adjustment: 24 Effective length of query: 219 Effective length of database: 220 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