GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Burkholderia phytofirmans PsJN

Align AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate BPHYT_RS31425 BPHYT_RS31425 arginine ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__BFirm:BPHYT_RS31425
          Length = 233

 Score =  254 bits (648), Expect = 1e-72
 Identities = 133/240 (55%), Positives = 167/240 (69%), Gaps = 8/240 (3%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           +E+ N++KWYG   VL D    + RGE +VI GPSGSGKST+I+ +N LE  Q G+IVVD
Sbjct: 2   IELNNVSKWYGGNRVLNDCTASIARGEVVVICGPSGSGKSTLIKSVNGLEAVQSGQIVVD 61

Query: 78  GTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFL 137
           G ++T     +  +R  VGMVFQHF LFPHL++  N  LA + V    + +A E A   L
Sbjct: 62  GIDVTAKRADLSRLRARVGMVFQHFELFPHLSVQRNLMLAQMNVLGRARDKAAERARLLL 121

Query: 138 KRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVG 197
            RV +    +KYP QLSGGQQQRVAIAR+L M+P  MLFDEPTSALDPEM+ EVLD    
Sbjct: 122 LRVGLSGHEHKYPAQLSGGQQQRVAIARALSMDPVAMLFDEPTSALDPEMVNEVLDV--- 178

Query: 198 LAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQILH 257
                MTMLCVTHEMGFA++VA+RV+FMD+G IVE +   AFF+ P+ ER + FLS+ILH
Sbjct: 179 -----MTMLCVTHEMGFAKRVADRVLFMDRGVIVEDDTREAFFERPRSERARDFLSRILH 233


Lambda     K      H
   0.321    0.135    0.394 

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: 175
Number of extensions: 4
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: 257
Length of database: 233
Length adjustment: 24
Effective length of query: 233
Effective length of database: 209
Effective search space:    48697
Effective search space used:    48697
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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