GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Methanobacterium veterum MK4

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_048080973.1 EJ01_RS11645 ABC transporter ATP-binding protein

Query= uniprot:P70970
         (276 letters)



>NCBI__GCF_000745485.1:WP_048080973.1
          Length = 222

 Score =  125 bits (313), Expect = 1e-33
 Identities = 83/208 (39%), Positives = 120/208 (57%), Gaps = 19/208 (9%)

Query: 9   ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLK-PTKGQISLGSTVIQAGKKNKDL 67
           AL  IN  + +GS++A++G +GSGKSTLL HL G+L  P+KG + L    I+    N+  
Sbjct: 24  ALRGINLKVNKGSFIAIMGPSGSGKSTLL-HLAGILDIPSKGTVLLNGKNIKEYTGNEQA 82

Query: 68  KKLRKKVGIVFQ----FPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSE 123
           +  RK +G +FQ     P+    E  +L  IS              +KA+E+L  VGLS+
Sbjct: 83  ELRRKNIGFIFQRYNLMPQLTALENVMLPMIS-----------PDSKKAKELLDKVGLSD 131

Query: 124 ELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGN 183
           +  DR   +LSGG+ +RVAIA  LA DP +L+ DEPT  LD    ++IM +  +L+Q   
Sbjct: 132 KY-DRYQTQLSGGEQQRVAIARALANDPSILLADEPTGELDTVNTRKIMGLLKDLNQEKG 190

Query: 184 LTTILVTHSMEDAAAYADEMIVMHKGTI 211
           LT I+VTH+   AA + +E+I M  G I
Sbjct: 191 LTIIIVTHN-PLAAEFVEEVIKMQDGDI 217


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: 139
Number of extensions: 7
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: 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