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_RS13580 BPHYT_RS13580 arginine ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__BFirm:BPHYT_RS13580
          Length = 248

 Score =  255 bits (651), Expect = 7e-73
 Identities = 125/238 (52%), Positives = 170/238 (71%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           +++ +++K + D HVL+ ++L V RG+ + + GPSGSGKST++RCIN LE H  G+I V+
Sbjct: 2   IKVDSIHKRFHDQHVLKGVSLNVERGQVVCLIGPSGSGKSTLLRCINGLERHDAGEITVE 61

Query: 78  GTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFL 137
           G  +    K+I E+R +VGMVFQ FNLFPH T LEN    P++V+K  + QA E A H L
Sbjct: 62  GRTVDAKSKQIHELRAQVGMVFQRFNLFPHRTALENVFEGPVFVKKQARAQARERARHLL 121

Query: 138 KRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVG 197
            +V +  + N +P +LSGGQQQRVAIAR+L M PK +LFDEPTSALDPE++ EVL  M  
Sbjct: 122 DKVGLAHRMNAHPAELSGGQQQRVAIARALAMEPKAILFDEPTSALDPELVGEVLGVMRQ 181

Query: 198 LAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQI 255
           LA++GMTM+ VTHEM FAR+VA+RV F+  G I E+   A  FD P+H RT+ FL ++
Sbjct: 182 LADDGMTMIVVTHEMAFAREVADRVCFLHDGAIHEEGSAAELFDRPRHARTREFLGKM 239


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: 203
Number of extensions: 7
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: 257
Length of database: 248
Length adjustment: 24
Effective length of query: 233
Effective length of database: 224
Effective search space:    52192
Effective search space used:    52192
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