GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Pseudomonas fluorescens FW300-N2C3

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 AO356_29680 AO356_29680 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_29680
          Length = 254

 Score =  257 bits (657), Expect = 1e-73
 Identities = 133/249 (53%), Positives = 176/249 (70%), Gaps = 12/249 (4%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           V+ V++NK+Y  FH L+DIN++V +GE + I GPSGSGKST++RC+N+LE+  KG + VD
Sbjct: 5   VKAVSLNKYYDQFHALKDINIEVEQGEVLCIIGPSGSGKSTLLRCVNQLEKIDKGGLWVD 64

Query: 78  GTELT------NDLKKIDEV-----RREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPK 126
           G EL       N L +++E      R   GMVFQ FNLFPH+T+L+N    P  V K   
Sbjct: 65  G-ELVGYRIVGNKLHELNETQIARQRLSTGMVFQRFNLFPHMTVLQNIIEGPCQVLKRSP 123

Query: 127 KQAEEVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPE 186
           K+A E A+  L RV + ++ N YP +LSGGQQQRVAIAR+L M PK+MLFDEPTSALDPE
Sbjct: 124 KEANEEALELLARVGLADKRNSYPIELSGGQQQRVAIARALAMRPKLMLFDEPTSALDPE 183

Query: 187 MIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHE 246
           ++ EVL  M  LA+ GMTM+ VTHE+GFAR+V+NR++FMD GQIVE   P     +PQ+ 
Sbjct: 184 LVGEVLSVMRDLAQTGMTMIVVTHELGFAREVSNRMVFMDGGQIVEAGSPEEILISPQNP 243

Query: 247 RTKLFLSQI 255
           RT+ F+S +
Sbjct: 244 RTQSFISAV 252


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: 223
Number of extensions: 6
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: 254
Length adjustment: 24
Effective length of query: 233
Effective length of database: 230
Effective search space:    53590
Effective search space used:    53590
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