GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artQ in Burkholderia phytofirmans PsJN

Align Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate BPHYT_RS13585 BPHYT_RS13585 amino acid ABC transporter permease

Query= TCDB::Q9HU30
         (231 letters)



>FitnessBrowser__BFirm:BPHYT_RS13585
          Length = 218

 Score =  124 bits (311), Expect = 1e-33
 Identities = 71/212 (33%), Positives = 118/212 (55%), Gaps = 11/212 (5%)

Query: 12  LLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLWVLMI 71
           LL G  +T++++  +  +  +LGLL A+ + S    +     T+  ++RG+P  + +  I
Sbjct: 13  LLKGAVVTIEITFCSFVLSTVLGLLLALMRVSDNRVVSNAAATFINVIRGLPIIVQLFYI 72

Query: 72  YFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHREAGQ 131
           YF        L DL     + LS F AG + LG+ +  Y  E FR  + +I  G  EA Q
Sbjct: 73  YF-------VLPDL----GVQLSAFQAGFIGLGIAYSVYQAENFRAGIQAIDHGQIEAAQ 121

Query: 132 ALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVASNATK 191
           ++G+    I  R+VLPQ +R+ALP  GN  +++LKD++L S IT+ E+ R  Q+ +++T 
Sbjct: 122 SIGMRGAMIMRRVVLPQAFRIALPPYGNTLVMMLKDSSLASTITVAEMTRAGQLIASSTF 181

Query: 192 EPFTFYMTAAAIYLSLTVVIMVALHFLERRAG 223
           +  T +   A +YL L++ ++  L  LERR G
Sbjct: 182 QNMTVFTLVALLYLGLSLPLVYGLRRLERRLG 213


Lambda     K      H
   0.327    0.143    0.431 

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: 97
Number of extensions: 5
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: 231
Length of database: 218
Length adjustment: 22
Effective length of query: 209
Effective length of database: 196
Effective search space:    40964
Effective search space used:    40964
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 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