GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltJ in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_5568 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)

Query= TCDB::Q9I403
         (248 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5568 Glutamate Aspartate
           transport system permease protein GltK (TC 3.A.1.3.4)
          Length = 223

 Score =  126 bits (317), Expect = 3e-34
 Identities = 70/212 (33%), Positives = 124/212 (58%), Gaps = 6/212 (2%)

Query: 28  GLGWTIAIALVGWIIALALGSLLGVMRTVPNRLVSGIATAYVEIFRNVPLLVQLFIWYFL 87
           G+  T+ +  +G +  + LG++L +MR   N+LVS IA AYV  FR++PLL+ +  +Y  
Sbjct: 18  GMVMTLKLMALGVVGGIILGTILALMRLSHNKLVSNIAGAYVNYFRSIPLLLVITWFYLA 77

Query: 88  VPDLLPEGLQTWFKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPYGQTSAARA 147
           VP +L      W   +  P   A+ S +V   +F AA  CE VR G+Q++P GQ  AA+A
Sbjct: 78  VPFVL-----RWITGEDTPI-GAFGSCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQA 131

Query: 148 MGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNIFKNSSVASLIGLMELLAQTKQTAEFSAN 207
           +G    Q  R ++LPQAFR + P L  + + +F+++S+   +GL++ L  ++ + +    
Sbjct: 132 LGMNYGQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNASRASGDIIGR 191

Query: 208 LFEAFTLATLIYFTLNMSLMLIMRLVERKVAV 239
             E   +A L+YFT++ +   +++ ++++ AV
Sbjct: 192 SNEFLIIAGLVYFTVSFAASQLVKRLQKRFAV 223


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: 159
Number of extensions: 4
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: 223
Length adjustment: 23
Effective length of query: 225
Effective length of database: 200
Effective search space:    45000
Effective search space used:    45000
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: 46 (22.3 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 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