GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF3102
          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 (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