GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3950 N515DRAFT_3950
           lipopolysaccharide export system ATP-binding protein
          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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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