GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Pseudomonas stutzeri RCH2

Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate GFF3102 Psest_3161 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= TCDB::Q88NY3
         (248 letters)



>FitnessBrowser__psRCH2:GFF3102
          Length = 365

 Score =  105 bits (263), Expect = 1e-27
 Identities = 71/213 (33%), Positives = 112/213 (52%), Gaps = 13/213 (6%)

Query: 28  GLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLFIWYFL 87
           GL  T+ IA      AL LG LL + R      +  +   ++E +R VPL+  LF+   +
Sbjct: 157 GLMLTVVIAAVGIAGALPLGILLALGRRSDMPAIRVLCVTFIEFWRGVPLITVLFMSSVM 216

Query: 88  VPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKGQEAAARA 147
           +P  LPEG+      +L+    A++ VV     F AA + E VR G+QA+PKGQ  AA A
Sbjct: 217 LPLFLPEGM------NLDKLLRAMLMVVF----FEAAYIAEVVRGGLQAIPKGQYEAAAA 266

Query: 148 MGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSAN 207
           MG    +    V+LPQA +++IP + + F+ +FK++S+  +IGL + L   K+     A 
Sbjct: 267 MGLGYWRSTLLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDFLNSIKRATADPAW 326

Query: 208 L---FEAFTLATLIYFTLNMGLMLLMRMVEKKV 237
           L    E +  A L+Y+    G+      +E+K+
Sbjct: 327 LGMSTEGYVFAALVYWMFCFGMSRYSMRLERKL 359


Lambda     K      H
   0.325    0.139    0.425 

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: 226
Number of extensions: 9
Number of successful extensions: 2
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: 248
Length of database: 365
Length adjustment: 27
Effective length of query: 221
Effective length of database: 338
Effective search space:    74698
Effective search space used:    74698
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 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