GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Phaeobacter inhibens BS107

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 GFF1143 PGA1_c11580 octopine permease ATP-binding protein P

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__Phaeo:GFF1143
          Length = 259

 Score =  207 bits (526), Expect = 2e-58
 Identities = 105/254 (41%), Positives = 160/254 (62%), Gaps = 10/254 (3%)

Query: 14  TEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGK 73
           T   +EI  ++K YG+  V++ +++   RG+ + + G SGSGKST++RC N LE+ Q+G 
Sbjct: 4   TTPVLEIRGLHKSYGELEVIKGVDITAHRGDVVSLIGSSGSGKSTLLRCCNLLEDSQEGD 63

Query: 74  IVVDGTELT----------NDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRK 123
           I+  G  +           +D K++  +R  + MVFQ FNL+ H+TIL+N   AP+ V  
Sbjct: 64  ILFKGEPINWSGTGLARRPSDAKQVLRIRTNLSMVFQQFNLWAHMTILQNVMEAPLTVLG 123

Query: 124 MPKKQAEEVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSAL 183
             + + E+ A  +L +V I ++ + YP QLSGGQQQR AIAR+LCM P+ +LFDEPTSAL
Sbjct: 124 RDRAEVEDAARKYLTKVGIGDKCDAYPAQLSGGQQQRAAIARALCMEPEALLFDEPTSAL 183

Query: 184 DPEMIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNP 243
           DPE+ +EV+  +  LA EG TM+ VTH+M  A  V++ ++F+ +G I E+  P   F + 
Sbjct: 184 DPELEQEVVKVIKDLAAEGRTMIIVTHDMNMAADVSSHIVFLHKGLIEEEGCPDEVFGST 243

Query: 244 QHERTKLFLSQILH 257
           + ER + FL+   H
Sbjct: 244 RSERLRGFLASTRH 257


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: 168
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: 259
Length adjustment: 24
Effective length of query: 233
Effective length of database: 235
Effective search space:    54755
Effective search space used:    54755
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: 47 (22.7 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