Align lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized)
to candidate BPHYT_RS10140 BPHYT_RS10140 ABC transporter substrate-binding protein
Query= CharProtDB::CH_003045 (260 letters) >FitnessBrowser__BFirm:BPHYT_RS10140 Length = 260 Score = 288 bits (738), Expect = 6e-83 Identities = 137/259 (52%), Positives = 185/259 (71%) Query: 1 MKKTVLALSLLIGLGATAASYAALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMC 60 MK + +LS+ + ++ + A TVR G D +Y PF SK A G+ +GFDIDLGNE+C Sbjct: 1 MKSLLASLSIALLAISSGNAIAKEWSTVRFGVDASYPPFESKSADGKLVGFDIDLGNEIC 60 Query: 61 KRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAK 120 +R+ KC WV + FD +IP+LK +K D ++S++S+T RQ +IAFS K++ +RL+A K Sbjct: 61 RRLNAKCVWVENAFDGMIPALKGRKFDGVLSTMSMTPARQAQIAFSSKVFRIPTRLVAKK 120 Query: 121 GSPIQPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAA 180 GS I PT E+LKGK +GV QGS QE YA W G +VAY +QDL+YSDL AGR+DA+ Sbjct: 121 GSTITPTPEALKGKRIGVEQGSIQETYAKTYWEPAGAVIVAYQDQDLVYSDLLAGRIDAS 180 Query: 181 LQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELR 240 LQ+ V A GFL+ P GK++AFAG ++ D K G GT +GLRK+DT+LKA DKA+ + R Sbjct: 181 LQNAVQADVGFLRTPRGKDFAFAGNALYDAKTLGSGTAIGLRKEDTDLKAQIDKAIADTR 240 Query: 241 QDGTYDKMAKKYFDFNVYG 259 DGTYD++AKKYFDF+VYG Sbjct: 241 ADGTYDRIAKKYFDFDVYG 259 Lambda K H 0.315 0.132 0.374 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: 230 Number of extensions: 8 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: 260 Length of database: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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