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_RS31740 RR42_RS31740 ABC transporter permease

Query= TCDB::Q52813
         (400 letters)



>FitnessBrowser__Cup4G11:RR42_RS31740
          Length = 222

 Score = 90.9 bits (224), Expect = 3e-23
 Identities = 64/205 (31%), Positives = 112/205 (54%), Gaps = 19/205 (9%)

Query: 196 ALVIAIVASII--IARWAHKRQAATGQPFHTVWTA-IALIVGLPLLVFVVSGFPLTFDVP 252
           ALV+  V  ++  I R   +R+   G     + TA +  I G PLLV +   F L F +P
Sbjct: 29  ALVLGCVMGLLVGIGRLDPRRRVVYG-----LCTAYVTAIRGTPLLVQL---FLLFFGLP 80

Query: 253 VAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSS 312
              +F+     ++ P F+   + L  Y+ ++++EIVRG I+ V KGQ EAA ++G+    
Sbjct: 81  ---QFD-----ILLPAFVCGVIGLGIYSGAYVSEIVRGAIQSVDKGQMEAARSIGMSSGQ 132

Query: 313 VTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCI 372
             R V++PQA+  +IPPL ++++ L KNS+L   +   D++  G  I++ S +++E+   
Sbjct: 133 AMRAVILPQAIVRMIPPLGNEFIALIKNSALVSLLTIHDVMHEGQKIISVSYRSLEVYLA 192

Query: 373 WGIVYLSLSILTSLFMNWFNAKMAL 397
             +VYL L+    LF+     ++ +
Sbjct: 193 IALVYLLLTSAAGLFLRHMEQRLRM 217



 Score = 40.8 bits (94), Expect = 4e-08
 Identities = 44/150 (29%), Positives = 64/150 (42%), Gaps = 31/150 (20%)

Query: 99  TLLVAVTGIFTATIIGFLIGIGRLS-RNWLIAKLCTVYVEVFRNIPPLLVIFFWYLGVLS 157
           T+ V    +    ++G L+GIGRL  R  ++  LCT YV   R  P L+ +F  + G   
Sbjct: 22  TVEVTACALVLGCVMGLLVGIGRLDPRRRVVYGLCTAYVTAIRGTPLLVQLFLLFFG--- 78

Query: 158 VLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGI---ALVIAIVASIIIARWAHKR 214
            LPQ        F + L         P F  G+I +GI   A V  IV   I +    + 
Sbjct: 79  -LPQ--------FDILL---------PAFVCGVIGLGIYSGAYVSEIVRGAIQSVDKGQM 120

Query: 215 QAA------TGQPFHTVWTAIALIVGLPLL 238
           +AA      +GQ    V    A++  +P L
Sbjct: 121 EAARSIGMSSGQAMRAVILPQAIVRMIPPL 150


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: 258
Number of extensions: 15
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 400
Length of database: 222
Length adjustment: 26
Effective length of query: 374
Effective length of database: 196
Effective search space:    73304
Effective search space used:    73304
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