GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Dinoroseobacter shibae DFL-12

Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate 3606947 Dshi_0375 ABC transporter related (RefSeq)

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__Dino:3606947
          Length = 273

 Score =  175 bits (444), Expect = 8e-49
 Identities = 90/249 (36%), Positives = 146/249 (58%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           L+    +   FGG+ A+++   ++ +G I  +IGPNGAGK+++ N++S F  P +G+V+F
Sbjct: 21  LMEMRNITLKFGGVTAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQEGQVMF 80

Query: 71  DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130
            G P  +++P+Q+A+QG+ RTFQ       +SVL+N++         N     +      
Sbjct: 81  RGAPRPKMKPYQVARQGIARTFQNIALFEGMSVLDNIMTGRLTHMKSNMLDQAIWWGKAQ 140

Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190
           KEE + +E+   +++ + +        G L  G +K +E+ RAL   PKL+LLDEP AG+
Sbjct: 141 KEETENREKVEKIIDFLEIQNIRKTPVGRLPYGLKKRVELARALAAEPKLLLLDEPMAGM 200

Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250
           N    +D+   IL  N + G T  +IEH+M V+M L DRV V+  G+ + DGTP E++ N
Sbjct: 201 NVEEKEDMSRYILDTNDEFGTTIALIEHDMGVVMDLSDRVVVMDYGKKIGDGTPDEVRNN 260

Query: 251 SQVLEAYLG 259
             V++AYLG
Sbjct: 261 QDVIDAYLG 269


Lambda     K      H
   0.319    0.136    0.391 

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: 170
Number of extensions: 9
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: 260
Length of database: 273
Length adjustment: 25
Effective length of query: 235
Effective length of database: 248
Effective search space:    58280
Effective search space used:    58280
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 (21.7 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