GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Shewanella oneidensis MR-1

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 203044 SO3960 ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__MR1:203044
          Length = 243

 Score =  142 bits (357), Expect = 9e-39
 Identities = 84/249 (33%), Positives = 131/249 (52%), Gaps = 15/249 (6%)

Query: 12  LAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFD 71
           L A  L KS+   + V++  + V  G + GL+GPNGAGKTT F ++   ++ DKG +  D
Sbjct: 6   LKAQNLAKSYKSRQVVKDVSLTVKTGQVVGLLGPNGAGKTTTFYMVVGLVKSDKGHIFID 65

Query: 72  GEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVK 131
            + +     H  A++G+    Q A    +L+V +N++   Q +   N             
Sbjct: 66  DDDLTADPMHLRARKGIGYLPQEASIFRKLTVHDNIMAVLQTRKELN------------- 112

Query: 132 EEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVN 191
              Q +E    LLE   +          LSGG+R+ +E+ RAL  NPK ILLDEP AGV+
Sbjct: 113 -SDQREEALEQLLEEFHITHIRDSQGMSLSGGERRRVEIARALAANPKFILLDEPFAGVD 171

Query: 192 PRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNS 251
           P  + DI  +I+   +  G+  LI +HN+   + +C+  ++++ G  +A+GTPAEI  N 
Sbjct: 172 PISVIDI-KKIIEQLKSRGLGVLITDHNVRETLDVCEHAYIVSHGSLIAEGTPAEILDNQ 230

Query: 252 QVLEAYLGK 260
           QV   YLG+
Sbjct: 231 QVRAVYLGE 239


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: 133
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: 260
Length of database: 243
Length adjustment: 24
Effective length of query: 236
Effective length of database: 219
Effective search space:    51684
Effective search space used:    51684
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: 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