GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltL in Pseudomonas stutzeri RCH2

Align Amino acid ABC transporter ATP binding 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 GFF4241 Psest_4314 ABC-type metal ion transport system, ATPase component

Query= TCDB::Q9I405
         (244 letters)



>lcl|FitnessBrowser__psRCH2:GFF4241 Psest_4314 ABC-type metal ion
           transport system, ATPase component
          Length = 335

 Score =  172 bits (435), Expect = 1e-47
 Identities = 103/231 (44%), Positives = 140/231 (60%), Gaps = 8/231 (3%)

Query: 1   MISIKNVSKWYG----DFQVLTDCSTEVAKGEVVVVCGPSGSGKSTLIKCVNALEPFQKG 56
           MI    V K Y     D   L     E+A GEV  + G SG+GKSTL++ +N LE    G
Sbjct: 1   MIEFHQVHKTYRTGGRDVPALQPTQLEIASGEVFGLIGHSGAGKSTLLRLINRLEEPSGG 60

Query: 57  DIVVDGTSI-ADPKTNLPKLRSRVGMVFQHFELFPHLSITENLTIAQIKVLG-RSKEEAT 114
            I+V+G  + A     L + R RVGM+FQHF L    ++ +N+ +  +++ G RS+ E  
Sbjct: 61  RILVNGEDVTALDADGLRRFRQRVGMIFQHFNLLMSKTVADNVAMP-LRLAGIRSRREID 119

Query: 115 KKGLALLERVGLKEHAHKHPGQLSGGQQQRVAIARALAMDPVVMLFDEPTSALDPEMVNE 174
            +  ALLERVGLKEHA K+P QLSGGQ+QRV IARALA +P ++L DE TSALDP+    
Sbjct: 120 ARVAALLERVGLKEHARKYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPQTTAS 179

Query: 175 VLDVMVQLAHE-GMTMMCVTHEMGFARKVANRVIFMDRGQIVEDCEKEEFF 224
           VL ++ ++  E  +T++ +THEM   R+V +RV  MD G IVE     E F
Sbjct: 180 VLQLLAEINRELKLTIVLITHEMDVIRRVCDRVAVMDAGAIVEQGPVTEVF 230


Lambda     K      H
   0.320    0.135    0.389 

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: 211
Number of extensions: 10
Number of successful extensions: 4
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: 244
Length of database: 335
Length adjustment: 26
Effective length of query: 218
Effective length of database: 309
Effective search space:    67362
Effective search space used:    67362
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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, 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