GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Flavobacterium beibuense F44-8

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_035130886.1 Q763_RS02520 ABC transporter ATP-binding protein

Query= uniprot:P70970
         (276 letters)



>NCBI__GCF_000769915.1:WP_035130886.1
          Length = 222

 Score =  119 bits (297), Expect = 7e-32
 Identities = 76/209 (36%), Positives = 123/209 (58%), Gaps = 14/209 (6%)

Query: 10  LYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGK-----KN 64
           L  ++  IK+G  V+++G +G+GK+TLLQ L  L KP   +   G++++  G+     K+
Sbjct: 17  LKGVDLHIKKGEVVSIVGASGAGKTTLLQILGTLDKPKSEK---GTSLLIDGEDVLNMKD 73

Query: 65  KDLKKLRK-KVGIVFQFPEHQLFEE-TVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLS 122
           K L K R  K+G +FQF  HQLF E T L+++       G +K + E +A+++L+ +GLS
Sbjct: 74  KALSKFRNLKLGFIFQF--HQLFPEFTALENVCIPAFIAGKQKAETEAEAKKLLEYLGLS 131

Query: 123 EELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRG 182
             + +  P ELSGG+ +RVA+A  L   P V+  DEP+  LD    + + ++F++L    
Sbjct: 132 HRI-NHKPGELSGGEQQRVAVARALINKPAVIFADEPSGNLDTHSAENLHNLFFKLRDEM 190

Query: 183 NLTTILVTHSMEDAAAYADEMIVMHKGTI 211
             T ++VTH+ E+ A  AD  +VM  G I
Sbjct: 191 GQTFVIVTHN-EELANMADRKLVMSDGQI 218


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: 146
Number of extensions: 6
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: 222
Length adjustment: 24
Effective length of query: 252
Effective length of database: 198
Effective search space:    49896
Effective search space used:    49896
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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