GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_21715
          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.

Links

Downloads

Related tools

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