GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Shewanella amazonensis SB2B

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 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__SB2B:6938538
          Length = 378

 Score =  149 bits (375), Expect = 1e-40
 Identities = 83/250 (33%), Positives = 137/250 (54%), Gaps = 6/250 (2%)

Query: 7   KKLTVSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRL 66
           K  T +  EV ++I  ++K + D   + D++L + +GE   + G SGSGKST++R +   
Sbjct: 10  KPTTKTQDEVLLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGF 69

Query: 67  EEHQKGKIVVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPK 126
           E   +G+I +DG ++T+    +    R + M+FQ + LFPH+T+ +N     +   KM K
Sbjct: 70  ERPTEGRIYLDGQDITD----LPPYERPINMMFQSYALFPHMTVEQNIAFG-LKQDKMSK 124

Query: 127 KQAEEVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPE 186
               +     LK V + + A + P QLSGGQ+QRVA+ARSL   PK++L DEP  ALD +
Sbjct: 125 ADISQRVQEMLKLVHMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKK 184

Query: 187 MIKEV-LDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQH 245
           +  ++ L+ +  L   G+T + VTH+   A  +A R+  M  G I +   P   +++P  
Sbjct: 185 LRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIYESPNS 244

Query: 246 ERTKLFLSQI 255
                F+  +
Sbjct: 245 RMIAEFIGTV 254


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: 214
Number of extensions: 11
Number of successful extensions: 4
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: 378
Length adjustment: 27
Effective length of query: 230
Effective length of database: 351
Effective search space:    80730
Effective search space used:    80730
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: 48 (23.1 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