GapMind for catabolism of small carbon sources

 

Alignments for a candidate for argT in Burkholderia phytofirmans PsJN

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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