GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Paraburkholderia phymatum STM815

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 WP_012401946.1 BPHY_RS13050 amino acid ABC transporter permease

Query= TCDB::Q52813
         (400 letters)



>NCBI__GCF_000020045.1:WP_012401946.1
          Length = 246

 Score = 90.5 bits (223), Expect = 5e-23
 Identities = 66/213 (30%), Positives = 106/213 (49%), Gaps = 9/213 (4%)

Query: 188 TGMIAVGIALVIAIVASI--IIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGF 245
           T  +++   ++  IV S+  ++    +K+ AA G  +  ++  I LIV   +   V+   
Sbjct: 33  TVTVSLSAWVIALIVGSLFGVLRTVPNKKLAAIGTVYVAIFRNIPLIVQFFIWYLVI--- 89

Query: 246 PLTFDVPVAGKFN-LTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAG 304
           P    V +   F  L  G+     F S  + L  +TA+ + E VR GI  +P+GQ  A  
Sbjct: 90  PELLPVSIGTWFKQLPPGAQF---FSSSIICLGLFTAARVCEQVRSGINALPRGQRGAGL 146

Query: 305 ALGLHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSG 364
           ALG       R V++P A RII+PPLTS++LN+ KNS++A  IG  DL A    +++ + 
Sbjct: 147 ALGFTQWQTYRYVLLPVAYRIIVPPLTSEFLNIFKNSAVASTIGLLDLSAQARQLVDYTA 206

Query: 365 QAIEIVCIWGIVYLSLSILTSLFMNWFNAKMAL 397
           Q  E      + YL ++++    M    AK  L
Sbjct: 207 QTYESFIAVTVAYLLINLIVMTLMRIVEAKSRL 239



 Score = 57.8 bits (138), Expect = 3e-13
 Identities = 31/83 (37%), Positives = 48/83 (57%)

Query: 78  SLITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVE 137
           S ++    +TY   LL G+  T+ V+++    A I+G L G+ R   N  +A + TVYV 
Sbjct: 12  SPVSTGEPTTYLGWLLSGLWVTVTVSLSAWVIALIVGSLFGVLRTVPNKKLAAIGTVYVA 71

Query: 138 VFRNIPPLLVIFFWYLGVLSVLP 160
           +FRNIP ++  F WYL +  +LP
Sbjct: 72  IFRNIPLIVQFFIWYLVIPELLP 94


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: 288
Number of extensions: 16
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: 246
Length adjustment: 27
Effective length of query: 373
Effective length of database: 219
Effective search space:    81687
Effective search space used:    81687
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 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