GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12640 in Methylocella silvestris BL2

Align D-lactate transporter, ATP-binding component (characterized)
to candidate WP_012589117.1 MSIL_RS00330 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF1248
         (251 letters)



>NCBI__GCF_000021745.1:WP_012589117.1
          Length = 265

 Score =  157 bits (396), Expect = 3e-43
 Identities = 87/250 (34%), Positives = 147/250 (58%), Gaps = 6/250 (2%)

Query: 3   ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62
           +L +K +  R+GGL A+ D++L V E  + A+IGPNGAGK++L N + G    D G +  
Sbjct: 6   LLNIKGLTLRYGGLAAVEDLDLIVAEGALDALIGPNGAGKTSLFNLISGLTRQDDGEIWL 65

Query: 63  DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAV--- 119
            G  +   +P +  + G++R FQ   +F + + +EN+++       G+  +  ++     
Sbjct: 66  GGARIDRLSPSQRARRGLARTFQNLRLFTETTAIENVLVGMHLHVGGSL-LEILTRFGRF 124

Query: 120 -SGQRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAG 178
              +R  ++ A  +L  + ++   +  A S+S GD+RRLEI   L+ +P+LLLLDEP AG
Sbjct: 125 RQAERAAVDAARELLAFVGLSSVEYAPAGSLSYGDQRRLEIARALAAKPKLLLLDEPAAG 184

Query: 179 MARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKG 238
           M  A+T     LL+++++++ I++ ++EHDM +V  L D+ITVL  G  + E  P  ++ 
Sbjct: 185 MNPAETAALRLLLEKLRAQK-ISMLLVEHDMSLVMRLCDKITVLNFGRKIAEGPPDAVRA 243

Query: 239 NPKVREAYLG 248
           NP V EAYLG
Sbjct: 244 NPAVIEAYLG 253


Lambda     K      H
   0.318    0.135    0.379 

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: 155
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: 251
Length of database: 265
Length adjustment: 24
Effective length of query: 227
Effective length of database: 241
Effective search space:    54707
Effective search space used:    54707
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