GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bgtB' in Pseudomonas fluorescens FW300-N2E3

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate AO353_21715 AO353_21715 amino acid ABC transporter permease

Query= uniprot:Q31RP0
         (377 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_21715 AO353_21715 amino acid
           ABC transporter permease
          Length = 220

 Score = 85.1 bits (209), Expect = 2e-21
 Identities = 51/157 (32%), Positives = 88/157 (56%), Gaps = 9/157 (5%)

Query: 215 VTVLMLLTQLSWPQQLQPGQIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAG 274
           + VL+LL   + P          G+RL  +  + ++ L  Y GA++TE+ RGG+LS+P G
Sbjct: 69  ILVLILLIYFALPSL--------GIRLD-KLPSFIITLSLYAGAYLTEVFRGGLLSIPKG 119

Query: 275 QWEAAAALGLTRSQTLWQIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQT 334
             EA  A+GL   Q    + VP  LR ++P+L++ ++   K++SLA A+  P+L   A+ 
Sbjct: 120 LREAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARK 179

Query: 335 TLNQTGRPVEVFLILMLTYLAINAVISAGMNGLQQRL 371
              ++ R +E +L+    Y+A   +I+  +  L+QRL
Sbjct: 180 INVESYRVIETWLVTTALYVAACYLIAMLLRYLEQRL 216



 Score = 47.0 bits (110), Expect = 5e-10
 Identities = 30/77 (38%), Positives = 44/77 (57%), Gaps = 4/77 (5%)

Query: 69  AIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAV 128
           A  +R  D+    L +GL  +L  IAIG     VIG L   A  S++  LR L+  YV V
Sbjct: 8   AAVWRDFDTLLAGLGLGLELALVSIAIGC----VIGLLMAFALLSKHRALRVLASVYVTV 63

Query: 129 VRNTPLLLQLIVWYFPI 145
           +RNTP+L+ +++ YF +
Sbjct: 64  IRNTPILVLILLIYFAL 80


Lambda     K      H
   0.326    0.140    0.445 

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: 245
Number of extensions: 16
Number of successful extensions: 3
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: 377
Length of database: 220
Length adjustment: 26
Effective length of query: 351
Effective length of database: 194
Effective search space:    68094
Effective search space used:    68094
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: 47 (22.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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