GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltJ in Marinobacter adhaerens HP15

Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate GFF3090 HP15_3033 amino acid ABC transporter, inner membrane subunit

Query= TCDB::Q88NY3
         (248 letters)



>FitnessBrowser__Marino:GFF3090
          Length = 240

 Score = 92.8 bits (229), Expect = 6e-24
 Identities = 64/212 (30%), Positives = 105/212 (49%), Gaps = 8/212 (3%)

Query: 25  YITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLFIW 84
           Y  G+  T+ +   + +I LL+   L ++RTV N  VSG    Y  LFR  PLL+QL+I 
Sbjct: 23  YWDGMVTTVHLVFLSLVIGLLVAVPLAILRTVRNPFVSGPVWLYTYLFRGTPLLIQLYII 82

Query: 85  YFLVPDLLPEGLQE--WFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKGQE 142
           Y+ +  +  EG+QE  W++    P   AL++      L TAA   E +R  I + P G+ 
Sbjct: 83  YYGLAQI--EGIQETFWWEIFREPFYPALLAFT----LNTAAYTTEIIRGAIISTPNGEI 136

Query: 143 AAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTA 202
            AA+A G +       ++LP A R  +   ++E + +   S++AS++ +++L    +   
Sbjct: 137 EAAKAYGMNWFMRMRRIVLPSAARRAVQAYSNEVIFMLHASAIASVVTIVDLTGAARNIY 196

Query: 203 EFSANLFEAFTLATLIYFTLNMGLMLLMRMVE 234
                 F+AF    L Y  L   L+   R +E
Sbjct: 197 SRFYAPFDAFIFVALCYMALTFILVFAFRKLE 228


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: 144
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: 240
Length adjustment: 24
Effective length of query: 224
Effective length of database: 216
Effective search space:    48384
Effective search space used:    48384
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