GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_04267 H281DRAFT_04267 L-glutamate ABC transporter ATP-binding protein /L-aspartate ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__Burk376:H281DRAFT_04267
          Length = 241

 Score =  285 bits (728), Expect = 8e-82
 Identities = 142/240 (59%), Positives = 181/240 (75%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           + I N++KWYG F VL D   +V +GE +V+ GPSGSGKST+I+ +N LE  QKG+IV++
Sbjct: 2   ISIKNVSKWYGQFQVLTDCTTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPFQKGEIVIN 61

Query: 78  GTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFL 137
           G  LT+    + ++R +VGMVFQHF LFPHL+I++N TLA I V    K +A    +  L
Sbjct: 62  GQSLTDKKTNLSKLRSKVGMVFQHFELFPHLSIVQNLTLAQIKVLGRSKDEASAKGLKLL 121

Query: 138 KRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVG 197
            RV +   A+K+PGQLSGGQQQRVAIAR+L M+P  MLFDEPTSALDPEMI EVLD MV 
Sbjct: 122 DRVGLRAHADKFPGQLSGGQQQRVAIARALSMDPIAMLFDEPTSALDPEMINEVLDVMVE 181

Query: 198 LAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQILH 257
           LA+EGMTM+CVTHEMGFA++VA+RVIFMD+G IVE +    FF NP+ +R K FL++ILH
Sbjct: 182 LAQEGMTMMCVTHEMGFAKKVAHRVIFMDKGLIVEDDRKEDFFANPKSDRAKDFLAKILH 241


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: 191
Number of extensions: 6
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: 241
Length adjustment: 24
Effective length of query: 233
Effective length of database: 217
Effective search space:    50561
Effective search space used:    50561
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