GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltJ in Pseudomonas stutzeri RCH2

Align Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate GFF3102 Psest_3161 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= TCDB::Q9I403
         (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 =  107 bits (266), Expect = 4e-28
 Identities = 75/225 (33%), Positives = 115/225 (51%), Gaps = 13/225 (5%)

Query: 16  IGSETYLDWYIAGLGWTIAIALVGWIIALALGSLLGVMRTVPNRLVSGIATAYVEIFRNV 75
           +G +T       GL  T+ IA VG   AL LG LL + R      +  +   ++E +R V
Sbjct: 145 LGLQTVPTSQWGGLMLTVVIAAVGIAGALPLGILLALGRRSDMPAIRVLCVTFIEFWRGV 204

Query: 76  PLLVQLFIWYFLVPDLLPEGLQTWFKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQ 135
           PL+  LF+   ++P  LPEG+      +L+    A L VV     F AA + E VR G+Q
Sbjct: 205 PLITVLFMSSVMLPLFLPEGM------NLDKLLRAMLMVV----FFEAAYIAEVVRGGLQ 254

Query: 136 ALPYGQTSAARAMGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNIFKNSSVASLIGLMELL 195
           A+P GQ  AA AMG    +    V+LPQA +++IP + + F+ +FK++S+  +IGL + L
Sbjct: 255 AIPKGQYEAAAAMGLGYWRSTLLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDFL 314

Query: 196 AQTKQTAEFSANL---FEAFTLATLIYFTLNMSLMLIMRLVERKV 237
              K+     A L    E +  A L+Y+     +      +ERK+
Sbjct: 315 NSIKRATADPAWLGMSTEGYVFAALVYWMFCFGMSRYSMRLERKL 359


Lambda     K      H
   0.327    0.141    0.433 

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: 270
Number of extensions: 19
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: 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 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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 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