GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Cupriavidus basilensis 4G11

Align AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate RR42_RS16450 RR42_RS16450 hypothetical protein

Query= TCDB::Q52813
         (400 letters)



>FitnessBrowser__Cup4G11:RR42_RS16450
          Length = 211

 Score = 89.0 bits (219), Expect = 1e-22
 Identities = 45/113 (39%), Positives = 76/113 (67%)

Query: 274 LALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIPPLTSQ 333
           +ALS  +A++ AEI+R GIR V +GQ EAA A+G+    + R V++PQA RI++PP    
Sbjct: 93  IALSMSSAAYNAEIIRAGIRAVHRGQREAAQAVGMTNPRILRHVILPQATRIVLPPYMGN 152

Query: 334 YLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSL 386
           +++ TK++SLA  I   +L+    TI + + +A+E++ I G +YL+L+ + +L
Sbjct: 153 FISHTKSTSLASVITVPELMLSAQTIYSSTYRAVEVLTIAGAIYLALTTVLTL 205



 Score = 45.8 bits (107), Expect = 1e-09
 Identities = 26/73 (35%), Positives = 38/73 (52%)

Query: 80  ITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVF 139
           I F     Y   LL   L T+L+AV      T+ G L+ +GR SR+ ++     +Y+ +F
Sbjct: 3   IDFVQVLPYLPILLKAALLTILLAVVTQVCGTVFGLLLALGRDSRHAVLRGAAFIYIWIF 62

Query: 140 RNIPPLLVIFFWY 152
           R  P LL +FF Y
Sbjct: 63  RGTPVLLHLFFVY 75


Lambda     K      H
   0.327    0.141    0.432 

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: 185
Number of extensions: 6
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 400
Length of database: 211
Length adjustment: 26
Effective length of query: 374
Effective length of database: 185
Effective search space:    69190
Effective search space used:    69190
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: 48 (23.1 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