GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS04345 CA265_RS04345 lipoprotein-releasing system ATP-binding protein LolD

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__Pedo557:CA265_RS04345
          Length = 216

 Score =  131 bits (330), Expect = 1e-35
 Identities = 80/218 (36%), Positives = 121/218 (55%), Gaps = 7/218 (3%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           ++   + K YG+  +L+ +N +V +GE + I GPSG+GKST++  +  L++   G + + 
Sbjct: 2   LKATGIRKSYGNLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLHILGTLDKPDDGSVQLK 61

Query: 78  GT---ELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAM 134
           GT   +L  DL       + +G VFQ  +L P  + +EN  + P ++ K  KKQAE  A 
Sbjct: 62  GTVINKLNGDLLSTFR-NQNIGFVFQFHHLLPEFSAIENICI-PAFIAKTNKKQAETRAF 119

Query: 135 HFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDT 194
             L    + ++A   P QLSGG+QQRVAIAR+L  NP I+L DEP+  LD E    +   
Sbjct: 120 ELLDLFGLKDRAQHKPNQLSGGEQQRVAIARALINNPSIILADEPSGNLDSENAAGLHQL 179

Query: 195 MVGLAEE-GMTMLCVTHEMGFARQVANRVIFMDQGQIV 231
            V L +    T + VTH    A+  ++RV+ M  G IV
Sbjct: 180 FVSLRDNFHQTFVIVTHNEHLAK-TSDRVVSMKDGLIV 216


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: 131
Number of extensions: 5
Number of successful extensions: 3
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: 216
Length adjustment: 23
Effective length of query: 234
Effective length of database: 193
Effective search space:    45162
Effective search space used:    45162
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