GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_3950 N515DRAFT_3950 lipopolysaccharide export system ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3950
          Length = 239

 Score =  137 bits (346), Expect = 2e-37
 Identities = 86/250 (34%), Positives = 135/250 (54%), Gaps = 15/250 (6%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           +L+A GL K F   + V++    + +G + GL+GPNGAGKTT F ++   I  D G +  
Sbjct: 1   MLSAEGLQKRFRTRQVVRDFAFSIREGEVVGLLGPNGAGKTTCFYMVVGLIEADAGTIKL 60

Query: 71  DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130
           D   I  L  H  A+ G+    Q      RL+V +N++  A  +  EN            
Sbjct: 61  DKYDITGLPMHARAKLGIGYLPQEPSVFRRLTVADNIM--AVLELRENL----------- 107

Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190
              KQ   +   LL+ + +A  A +    LSGG+R+ +E+ RAL   P+ +LLDEP AGV
Sbjct: 108 -SAKQRAGELESLLDELKIAHIADQRGISLSGGERRRVEIARALAAEPRYMLLDEPFAGV 166

Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250
           +P  + +I  RI+   ++ G+  LI +HN+   + +CDR ++L +G+ L+ GTPA I  +
Sbjct: 167 DPISVGEI-QRIVRHLKERGIGVLITDHNVRETLGICDRAYILNDGEVLSRGTPAHILAD 225

Query: 251 SQVLEAYLGK 260
            +V E YLG+
Sbjct: 226 EKVREVYLGR 235


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: 122
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: 239
Length adjustment: 24
Effective length of query: 236
Effective length of database: 215
Effective search space:    50740
Effective search space used:    50740
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.

Links

Downloads

Related tools

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