GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Methanobacterium lacus AL-21

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein

Query= uniprot:P70970
         (276 letters)



>NCBI__GCF_000191585.1:WP_013645374.1
          Length = 223

 Score =  118 bits (295), Expect = 1e-31
 Identities = 74/207 (35%), Positives = 119/207 (57%), Gaps = 9/207 (4%)

Query: 8   LALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDL 67
           +AL +++  I+ G  V++IG +GSGKSTLL  + GL K  +GQIS+    +     N DL
Sbjct: 22  IALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDKANEGQISVAGVNLM---DNSDL 78

Query: 68  KKLRK-KVGIVFQFPEHQLFEE-TVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEEL 125
              R  ++G VFQ   H L    TVL+++    +   +  +  E++A ++L+ V L E  
Sbjct: 79  SNFRSNEIGFVFQL--HNLIPNLTVLENVQIPLLGTDIDDKKMEERALKLLKSVNL-ENK 135

Query: 126 LDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLT 185
           +D+ P +LSGG+ +RVAIA  L   P +++ DEPT  LD   ++ I+ +  ++H++ N+T
Sbjct: 136 VDQKPTKLSGGERQRVAIARALVNHPSIILADEPTGALDSETQEVILKLLLDIHKKENVT 195

Query: 186 TILVTHSMEDAAAYADEMIVMHKGTIQ 212
            I+VTH     A  AD  I +  G I+
Sbjct: 196 LIMVTHE-PYVAKQADRSIYVLDGKIK 221


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: 148
Number of extensions: 9
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: 223
Length adjustment: 24
Effective length of query: 252
Effective length of database: 199
Effective search space:    50148
Effective search space used:    50148
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 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