GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Herbaspirillum seropedicae SmR1

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 HSERO_RS00320 HSERO_RS00320 peptide ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__HerbieS:HSERO_RS00320
          Length = 240

 Score =  258 bits (659), Expect = 8e-74
 Identities = 123/239 (51%), Positives = 176/239 (73%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           +++  + K +G  H+LR I+ ++   E + + GPSGSGKST +RC+N LEE   G I ++
Sbjct: 2   IKVNQLQKRFGQAHILRGIDCEIRAREVVCVIGPSGSGKSTFLRCLNGLEEVSDGDIFIE 61

Query: 78  GTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFL 137
           G +L +    ++ +R E+GMVFQ FNLFPH+T+LEN  +AP+ V+K+ +++A  VA   L
Sbjct: 62  GVKLNDPKVNLNALRAELGMVFQRFNLFPHMTVLENLIMAPMQVKKLSRREAVLVAEKLL 121

Query: 138 KRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVG 197
           ++V + ++ + +P QLSGGQQQRVAIAR+L M PK+MLFDEPTSALDPE++ EVL  M  
Sbjct: 122 QKVGLLDKIDAFPNQLSGGQQQRVAIARALAMEPKVMLFDEPTSALDPELVGEVLTVMKQ 181

Query: 198 LAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQIL 256
           LAEEGMTM+ VTHEMGFAR+V++RV+F+DQG I+E+  P     +P HERT+ FL ++L
Sbjct: 182 LAEEGMTMVVVTHEMGFAREVSDRVLFIDQGVIMEEGPPQQVLGDPHHERTRDFLRKVL 240


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: 213
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: 240
Length adjustment: 24
Effective length of query: 233
Effective length of database: 216
Effective search space:    50328
Effective search space used:    50328
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