GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_2542 Ga0059261_2542 ABC-type (unclassified) transport system, ATPase component

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__Korea:Ga0059261_2542
          Length = 258

 Score =  122 bits (305), Expect = 1e-32
 Identities = 78/255 (30%), Positives = 129/255 (50%), Gaps = 16/255 (6%)

Query: 6   SPPLPLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDK 65
           +PP   LA   + KS+     + +  + V +G + GL+GPNGAGKTT F  +   ++PD 
Sbjct: 16  TPPTSGLAVVSIAKSYDKRVVLSDVSLSVGKGEVVGLLGPNGAGKTTCFYSVMGLVKPDA 75

Query: 66  GRVIFDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQ 125
           GR++ DG  I  L  ++ A  G+    Q       L+V +N+    +            +
Sbjct: 76  GRIMLDGVDITPLPMYRRAILGLGYLPQETSIFRGLTVAKNISAVLELS----------E 125

Query: 126 PQVVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDE 185
           P    +  +  Q     LLE  GL +     A  LSGG+R+  E+ RAL  +P ++LLDE
Sbjct: 126 PDKSARAARLDQ-----LLEEFGLTRLRDAPAMALSGGERRRAEIARALAADPSIMLLDE 180

Query: 186 PAAGVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPA 245
           P AG++P  I DI D +     ++ +  LI +HN+   + + DR  ++ +G+ L  G+P 
Sbjct: 181 PFAGIDPISIADIRDLVKELKTRN-IGVLITDHNVRETLDIVDRASIIYDGRVLFAGSPE 239

Query: 246 EIQTNSQVLEAYLGK 260
           ++  ++ V   YLG+
Sbjct: 240 DLVADANVRRLYLGE 254


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: 135
Number of extensions: 7
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: 258
Length adjustment: 24
Effective length of query: 236
Effective length of database: 234
Effective search space:    55224
Effective search space used:    55224
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