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_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein

Query= uniprot:P70970
         (276 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1562
          Length = 384

 Score =  129 bits (323), Expect = 1e-34
 Identities = 83/218 (38%), Positives = 127/218 (58%), Gaps = 14/218 (6%)

Query: 9   ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68
           AL D +  I EG +VA++G +GSGKS+LL+ L GL  P +G +    T + A      L 
Sbjct: 17  ALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRDGTDLLA------LP 70

Query: 69  KLRKKVGIVFQFPEHQLFEE-TVLKDISFG----PMNFGVKKEDAEQKAREMLQLVGLSE 123
             R+ +G+VFQ   + LF   TV  +I+FG    P      + D   +  ++L+ V L E
Sbjct: 71  AQRRDIGLVFQ--HYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLLRRVQL-E 127

Query: 124 ELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGN 183
           EL  R P +LSGGQ +RVA+A  LA++P +L+LDEP   LD + R  +     +L +   
Sbjct: 128 ELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRDLQRSLG 187

Query: 184 LTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221
           LTT+LVTH  ++A   AD ++VM++G I+  G+P +++
Sbjct: 188 LTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIY 225


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: 239
Number of extensions: 13
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: 384
Length adjustment: 28
Effective length of query: 248
Effective length of database: 356
Effective search space:    88288
Effective search space used:    88288
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