GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Pseudomonas simiae WCS417

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 GFF3453 PS417_17675 ABC transporter

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__WCS417:GFF3453
          Length = 249

 Score =  154 bits (389), Expect = 2e-42
 Identities = 97/256 (37%), Positives = 147/256 (57%), Gaps = 18/256 (7%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           LL    L  ++G   AV    ++V  G+I  +IGPNGAGKT+LF+ L+   +   G + F
Sbjct: 4   LLETKDLELAYGAFHAVNGVNLKVEAGTIHTIIGPNGAGKTSLFHCLTGERQATAGAIHF 63

Query: 71  DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGE---NFWQVQLQPQ 127
           DG+ + +   H     GM R+FQ+      LSV EN+ LAAQ + G    NFW+      
Sbjct: 64  DGKNLMRKPAHGRVGLGMARSFQLTSLFQNLSVRENLRLAAQGRDGARALNFWR------ 117

Query: 128 VVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPA 187
             V  +++  E A  +LE + L  +A   AG LS GQ+++LE+G ++ + PKL++LDEP 
Sbjct: 118 -RVDSKREHLEMADQVLERLQLTARADTLAGELSHGQQRVLEVGMSICSKPKLLMLDEPT 176

Query: 188 AGVNPRLIDDICDRILTWNRQD---GMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTP 244
           +G+    IDDI   I+T    D     T L+IEHNM ++MS+  R+ V++ GQ L +GTP
Sbjct: 177 SGMG---IDDI--PIMTQLISDLGRDHTVLLIEHNMSIVMSISQRITVMSHGQILVEGTP 231

Query: 245 AEIQTNSQVLEAYLGK 260
             ++ + +V  AYLG+
Sbjct: 232 EFVRADERVRTAYLGE 247


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: 152
Number of extensions: 8
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: 249
Length adjustment: 24
Effective length of query: 236
Effective length of database: 225
Effective search space:    53100
Effective search space used:    53100
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