GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Pseudomonas fluorescens FW300-N2E2

Align TRAP dicarboxylate transporter, DctP subunit (characterized, see rationale)
to candidate Pf6N2E2_487 TRAP-type C4-dicarboxylate transport system, periplasmic component

Query= uniprot:Q88NN8
         (323 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_487
          Length = 322

 Score =  518 bits (1334), Expect = e-152
 Identities = 255/323 (78%), Positives = 283/323 (87%), Gaps = 1/323 (0%)

Query: 1   MTFKRKLLLAVLPFAFSVAMPASALDIKFAEIHPAGYPTVVAEQNMGKKLEDASNGEITF 60
           M FKR LL+A LP AF +A  A ALDIK A+IHP GYPTVVAE++MGK LE  SNGE+ F
Sbjct: 1   MNFKRTLLIAALPLAF-LAQAAHALDIKIADIHPKGYPTVVAEESMGKTLEKESNGELKF 59

Query: 61  KMFAGGVLGSEKEVIEQAQIGAVQMTRVSLGIVGPVVPDVNVFNMPFVFRDHDHMRKIID 120
           K F GGVLGSEKEVIEQ Q GAVQM+RVSLGIVGPVVPDVNVFNMPF+FRD  HMR +ID
Sbjct: 60  KYFPGGVLGSEKEVIEQMQTGAVQMSRVSLGIVGPVVPDVNVFNMPFIFRDQAHMRAVID 119

Query: 121 GEIGQEILDKITNSDFNLVALAWMDGGSRSIYTKKPVRSLEDLKGMKIRVQGNPLFIDMM 180
           G++G  ILD+ITNS+F LVALAWMDGG+R++YTKKPV  LEDLKGMKIRVQGNP+FI+  
Sbjct: 120 GDVGDAILDRITNSEFGLVALAWMDGGTRNLYTKKPVHKLEDLKGMKIRVQGNPMFIETF 179

Query: 181 NAMGGNGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHFQSAKYYTLTGHLILPEPVVM 240
           NAMG NGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNH+Q+AKYY+LTGHLILPEP+VM
Sbjct: 180 NAMGANGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHYQNAKYYSLTGHLILPEPIVM 239

Query: 241 SKTTWNKLSPEQQALVKKVAREAQMEERALWDAKSAASEEKLKAAGVEFITVDKKPFYDA 300
           SK TWNKL+PEQQ +VKK A+ AQ EER LWD KS ASEEKLKAAGVEFITVDKKPFYDA
Sbjct: 240 SKITWNKLTPEQQDMVKKAAKAAQAEERVLWDKKSTASEEKLKAAGVEFITVDKKPFYDA 299

Query: 301 TASVREKYGAQYADLMKRIDAVQ 323
           TA +R KYGA YADL+KRI+AVQ
Sbjct: 300 TAPIRAKYGAPYADLIKRIEAVQ 322


Lambda     K      H
   0.318    0.134    0.381 

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: 358
Number of extensions: 12
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 323
Length of database: 322
Length adjustment: 28
Effective length of query: 295
Effective length of database: 294
Effective search space:    86730
Effective search space used:    86730
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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.

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