GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF3102 Psest_3161 amine acid ABC
           transporter, permease protein, 3-TM region,
           His/Glu/Gln/Arg/opine family
          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.

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 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, the preprint on GapMind for carbon sources, 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