GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Dyella japonica UNC79MFTsu3.2

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein

Query= uniprot:P70970
         (276 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1085
          Length = 336

 Score =  120 bits (301), Expect = 4e-32
 Identities = 75/216 (34%), Positives = 125/216 (57%), Gaps = 6/216 (2%)

Query: 9   ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68
           AL   +  I +G    +IGH+G+GKSTL++ +N L +P+ G I +  T + A   +  L+
Sbjct: 20  ALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGSILIDGTEMTA-LGDAALR 78

Query: 69  KLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAR--EMLQLVGLSEELL 126
             R+++G++FQ   + L  +TV  +I+F P+    + +  + KAR  E+L+ VGL E   
Sbjct: 79  AQRRRIGMIFQH-FNLLSSQTVADNIAF-PLRLAGETDAGKIKARVDELLRRVGL-EAHA 135

Query: 127 DRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTT 186
            + P +LSGGQ +RV IA  LA  P +L+ DE T+ LDP+    ++++  E+++   LT 
Sbjct: 136 SKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVLELLAEINRELKLTI 195

Query: 187 ILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFL 222
           +L+TH M+      D + V+  G I   G+  D+FL
Sbjct: 196 VLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFL 231


Lambda     K      H
   0.318    0.136    0.380 

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: 209
Number of extensions: 14
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: 276
Length of database: 336
Length adjustment: 27
Effective length of query: 249
Effective length of database: 309
Effective search space:    76941
Effective search space used:    76941
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.

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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