GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Novosphingobium fuchskuhlense FNE08-7

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 WP_067909264.1 AQZ52_RS02410 ATP-binding cassette domain-containing protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_001519075.1:WP_067909264.1
          Length = 327

 Score = 78.6 bits (192), Expect = 2e-19
 Identities = 62/230 (26%), Positives = 104/230 (45%), Gaps = 29/230 (12%)

Query: 12  LAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKG--RVI 69
           + A GL K F G  AV    I V +GSI G++GPNGAGKTT   +L   I PD G  RV+
Sbjct: 12  IEARGLVKRFDGFTAVDGVDISVPRGSIYGILGPNGAGKTTTLRMLLGIIDPDSGYRRVL 71

Query: 70  FDGEPIQQLQ--PHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQ 127
               P +  +   +   ++G+    + +  ++ L+ L  + L   ++ G +         
Sbjct: 72  GHERPTEVARRIGYLPEERGLYPAMKASEAIAFLAALRGVPLKEGRRRGRD--------- 122

Query: 128 VVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPA 187
                          LLE  GL   A      LS G  + +++   L+  P L++ DEP 
Sbjct: 123 ---------------LLEQHGLGYAADRQIRQLSKGMAQQVQLLGTLVHEPDLVVFDEPF 167

Query: 188 AGVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQ 237
           +G++  L     +R++    + G T +   H +     LCD++ ++A G+
Sbjct: 168 SGLD-ALNQGKLERMIRSLAERGTTVIFSTHVIAHAERLCDQIAIIAGGK 216


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: 153
Number of extensions: 4
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: 260
Length of database: 327
Length adjustment: 26
Effective length of query: 234
Effective length of database: 301
Effective search space:    70434
Effective search space used:    70434
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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