GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Cupriavidus basilensis 4G11

Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate RR42_RS02585 RR42_RS02585 amino acid ABC transporter permease

Query= TCDB::Q88NY3
         (248 letters)



>FitnessBrowser__Cup4G11:RR42_RS02585
          Length = 227

 Score =  118 bits (296), Expect = 9e-32
 Identities = 70/220 (31%), Positives = 121/220 (55%), Gaps = 5/220 (2%)

Query: 20  TYLDWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLV 79
           T LD    G+  ++ I +TA ++ ++ G++L +MR    +L++  A  YV +FR++PL++
Sbjct: 13  TTLDVLGEGMLVSLKITVTAVVVGIVWGTILAMMRLSSVKLLNWFAQGYVTIFRSIPLVM 72

Query: 80  QLFIWYFLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPK 139
            L  ++ ++P LL +        DL  T     S +I   LF AA   E +R GIQ++ +
Sbjct: 73  VLLWFFLIIPQLLQKAFNLSQASDLRMT-----SALIAFALFEAAYYSEIIRAGIQSVSR 127

Query: 140 GQEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTK 199
           GQ  AA+AMG +  Q    V+LPQA+R ++P L ++ + +F+++S+  +  L +   Q  
Sbjct: 128 GQMFAAQAMGMTYGQSMRLVILPQAFRNMVPLLLTQGIILFQDTSLVYVSALADFFGQAY 187

Query: 200 QTAEFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKVAV 239
              E    + E    A L+YF +     LL++  +KKVAV
Sbjct: 188 GIGERDGRIVEMLLFAGLVYFIICFSASLLVKRYQKKVAV 227


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: 150
Number of extensions: 6
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: 227
Length adjustment: 23
Effective length of query: 225
Effective length of database: 204
Effective search space:    45900
Effective search space used:    45900
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: 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:

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