GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Dyella japonica UNC79MFTsu3.2

Align TreV, component of Trehalose porter (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1085
          Length = 336

 Score =  135 bits (341), Expect = 1e-36
 Identities = 83/253 (32%), Positives = 135/253 (53%), Gaps = 10/253 (3%)

Query: 3   VELIDIVKKY---GKNI-VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGK 58
           +  +D+ K Y   GK+I  +   +  I  GE F I+G SG GKSTL++++  +E+   G 
Sbjct: 2   IRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGS 61

Query: 59  IIADGADITDKPP-----EKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKE-EIIER 112
           I+ DG ++T         ++R + M+FQ++ L  + +V DNIAFPL++ G     +I  R
Sbjct: 62  ILIDGTEMTALGDAALRAQRRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKAR 121

Query: 113 VEKAAKLLGISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTAR 172
           V++  + +G+     K   Q+SGGQ+QRV +ARA+   PS  L DE  S LD +   +  
Sbjct: 122 VDELLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVL 181

Query: 173 GELKRIQKELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQF 232
             L  I +ELK T + +TH+      + DR+A+L  G+  +      ++ +P+     +F
Sbjct: 182 ELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRRF 241

Query: 233 VGEFPMNFLPGEL 245
           V E       GEL
Sbjct: 242 VNEALPEEAAGEL 254


Lambda     K      H
   0.318    0.137    0.385 

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: 242
Number of extensions: 13
Number of successful extensions: 3
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: 324
Length of database: 336
Length adjustment: 28
Effective length of query: 296
Effective length of database: 308
Effective search space:    91168
Effective search space used:    91168
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: 49 (23.5 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