GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Magnetospirillum magneticum AMB-1

Align glucose transporter, ATPase component (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF3641
         (260 letters)



>NCBI__GCF_000009985.1:WP_011385004.1
          Length = 379

 Score = 97.4 bits (241), Expect = 4e-25
 Identities = 75/235 (31%), Positives = 113/235 (48%), Gaps = 22/235 (9%)

Query: 12  ATPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGE 71
           A PL+  + IS  FG   AV+HV + ++ GE   LLG +G GK+TL+++L+G      G 
Sbjct: 19  AVPLIRFEGISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGR 78

Query: 72  IRVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRE---LVTPFGLVDDSA 128
           I ++G  V    P +     +  ++Q+ AL  ++  A N+  G +   L  P  ++ D  
Sbjct: 79  ILIDGQDVTEVPPYE---RPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKP--VIKDKV 133

Query: 129 MEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGP-- 186
             A     M R +            LSGGQRQ VA+AR +    K++++DEP AAL    
Sbjct: 134 AAALELVQMGRFS------GRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKL 187

Query: 187 -HETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNG---QLVGTVDI 237
              TQ+  EL+      GI   ++ HD    M +  R  VM  G   Q+   VDI
Sbjct: 188 REATQL--ELVNIQDRVGITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDI 240


Lambda     K      H
   0.317    0.135    0.373 

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: 183
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: 260
Length of database: 379
Length adjustment: 27
Effective length of query: 233
Effective length of database: 352
Effective search space:    82016
Effective search space used:    82016
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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