GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Rhizorhabdus wittichii RW1

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= uniprot:P70970
         (276 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  140 bits (352), Expect = 3e-38
 Identities = 83/215 (38%), Positives = 132/215 (61%), Gaps = 8/215 (3%)

Query: 9   ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68
           AL +++  +  G  + + G +GSGKSTL++ +NGL    +G I +G   ++  ++   L+
Sbjct: 16  ALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVRPDRRV--LQ 73

Query: 69  KLRKKVGIVFQFPEHQLFEE-TVLKDISFGPMNF-GVKKEDAEQKAREMLQLVGLSEELL 126
           ++R +VG+VFQ  +  LF   T+L++ +  PM   G+ ++ AE  ARE+L+ V ++++  
Sbjct: 74  RIRARVGMVFQ--DFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRIADQA- 130

Query: 127 DRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTT 186
           D+ P +LSGGQ +R AIA  LAM PE+++ DEPT+ LD    KE++D+   L   G +T 
Sbjct: 131 DKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALATEG-ITM 189

Query: 187 ILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221
           + VTH M  A   AD +I M  G I  +GSPRD F
Sbjct: 190 LCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFF 224


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: 151
Number of extensions: 6
Number of successful extensions: 4
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: 241
Length adjustment: 24
Effective length of query: 252
Effective length of database: 217
Effective search space:    54684
Effective search space used:    54684
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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