GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Methanobacterium lacus AL-21

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein

Query= uniprot:P40735
         (281 letters)



>NCBI__GCF_000191585.1:WP_013645374.1
          Length = 223

 Score =  125 bits (315), Expect = 6e-34
 Identities = 80/221 (36%), Positives = 125/221 (56%), Gaps = 4/221 (1%)

Query: 1   MNQNQLISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLIL 60
           MN N +I ++++   Y +D    AL+ V L++  GE ++I+G +GSGKSTL   + GL  
Sbjct: 1   MNDNTIIKIKNLKKEY-EDGSIIALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDK 59

Query: 61  PESGDIEVAGIQLTEESVWEVRK--KIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREE 118
              G I VAG+ L + S     +  +IG VFQ   N     TV ++V   L    +  ++
Sbjct: 60  ANEGQISVAGVNLMDNSDLSNFRSNEIGFVFQL-HNLIPNLTVLENVQIPLLGTDIDDKK 118

Query: 119 MIERVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGR 178
           M ER    +K VN+++ +DQ+P  LSGG++QRVAIA  +   P II+ DE T  LD   +
Sbjct: 119 MEERALKLLKSVNLENKVDQKPTKLSGGERQRVAIARALVNHPSIILADEPTGALDSETQ 178

Query: 179 EEVLETVRHLKEQGMATVISITHDLNEAAKADRIIVMNGGK 219
           E +L+ +  + ++   T+I +TH+   A +ADR I +  GK
Sbjct: 179 EVILKLLLDIHKKENVTLIMVTHEPYVAKQADRSIYVLDGK 219


Lambda     K      H
   0.316    0.135    0.383 

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: 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: 281
Length of database: 223
Length adjustment: 24
Effective length of query: 257
Effective length of database: 199
Effective search space:    51143
Effective search space used:    51143
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 (21.6 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