GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Cupriavidus basilensis 4G11

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 RR42_RS29660 RR42_RS29660 amino acid transporter

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__Cup4G11:RR42_RS29660
          Length = 264

 Score =  237 bits (604), Expect = 2e-67
 Identities = 126/256 (49%), Positives = 171/256 (66%), Gaps = 12/256 (4%)

Query: 10  TVSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEH 69
           T  A    + + +++K +GD  VL+ ++L   +G+ I I G SGSGKST +RCIN LE  
Sbjct: 5   TTQAMSCKLAVQDIHKSFGDNEVLKGVSLTAKKGDVISIIGASGSGKSTFLRCINYLERP 64

Query: 70  QKGKIVVDGTEL------TNDL-----KKIDEVRREVGMVFQHFNLFPHLTILENCTLAP 118
           + G+I +DG E+      T DL     K++  +R ++ MVFQHFNL+ H+ +LEN   AP
Sbjct: 65  KSGQIFLDGEEIRTKKDKTGDLVVVEPKQLQRMRTKLSMVFQHFNLWAHMNVLENIIEAP 124

Query: 119 IWVRKMPKKQAEEVAMHFLKRVKIPEQANK-YPGQLSGGQQQRVAIARSLCMNPKIMLFD 177
             V  + +K+AEE A  +L++V +P +  K YP  LSGGQQQRVAIAR+L MNP +MLFD
Sbjct: 125 THVLGLSRKEAEERAREYLEKVGLPPRVEKQYPSHLSGGQQQRVAIARALAMNPDVMLFD 184

Query: 178 EPTSALDPEMIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPA 237
           EPTSALDPE++ EVL  M  LAEEG TM+ VTHEMGFAR V+N V+F+ QG+  EQ  P 
Sbjct: 185 EPTSALDPELVGEVLKVMQKLAEEGRTMIVVTHEMGFARNVSNHVMFLHQGRTEEQGPPE 244

Query: 238 AFFDNPQHERTKLFLS 253
              ++P+ ER + FLS
Sbjct: 245 EVLNSPRSERLRQFLS 260


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: 199
Number of extensions: 6
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: 264
Length adjustment: 25
Effective length of query: 232
Effective length of database: 239
Effective search space:    55448
Effective search space used:    55448
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