GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Dehalococcoides mccartyi 195

Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease

Query= TCDB::Q88NY3
         (248 letters)



>NCBI__GCF_000011905.1:WP_010936196.1
          Length = 273

 Score =  135 bits (340), Expect = 9e-37
 Identities = 80/248 (32%), Positives = 135/248 (54%), Gaps = 18/248 (7%)

Query: 5   WDW---GVFFKSTGV---GSETYLD---WYITGLGWTIAIAITAWIIALLLGSLLGVMRT 55
           W W   GVF  + G+     + +LD   +   G+G T+ +A+ ++ + L+LG    + R 
Sbjct: 27  WWWLVAGVFVLTGGLMLFQPDPFLDIFKYVWVGIGITVLVAVVSYFLMLILGMFGALGRL 86

Query: 56  VPNRLVSGIATAYVELFRNVPLLVQLFIWYFLVPDLLP---EGLQ--EWFKQDLNPTTSA 110
             N ++ G+AT YVE+ R +PLLVQL  WYF  P ++    +GL          NP   A
Sbjct: 87  SKNTILRGLATFYVEIVRGIPLLVQLIWWYFAFPVIIQSIGQGLNFGPMMNYQANPIVMA 146

Query: 111 LISVVICLGLFTAARVCEQVRTGIQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIP 170
           +  +  C G + +    E  R GIQ++PKGQ  AAR++G S  Q    V+LPQA R+++P
Sbjct: 147 IWGMTFCYGAYMS----EIYRAGIQSIPKGQMEAARSLGMSHTQAMRYVILPQALRVVLP 202

Query: 171 PLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMGLMLLM 230
           P+ +EF+ + K++S+ S + + +++   ++    + N  E +T+  L+Y  L +    L+
Sbjct: 203 PMGNEFIALLKDTSLVSTVAVADMVRLGREFTATNFNPIEVWTMIGLLYLILTLLSSRLI 262

Query: 231 RMVEKKVA 238
             +EKK A
Sbjct: 263 NYIEKKTA 270


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: 175
Number of extensions: 8
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: 273
Length adjustment: 24
Effective length of query: 224
Effective length of database: 249
Effective search space:    55776
Effective search space used:    55776
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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