GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Flavobacterium ummariense DS-12

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_091518158.1 BM253_RS01840 ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_900115115.1:WP_091518158.1
          Length = 249

 Score =  112 bits (280), Expect = 1e-29
 Identities = 70/227 (30%), Positives = 119/227 (52%), Gaps = 4/227 (1%)

Query: 4   LKLTGVEKAY--GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLE 61
           +K+  + K Y   D + L+N+ L+I Q  +   +GP+G GK+TL+ ++ G+ + T G+ E
Sbjct: 5   IKIQNISKQYKGADFQSLNNVVLNIPQQSVFGLLGPNGAGKTTLISILCGIIQPTLGSYE 64

Query: 62  IDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKL 121
           I+G    +    +  I +V Q YALYP +T  EN+ +   +   S+A++ A +      L
Sbjct: 65  INGISNKNTSSIKNIIGVVPQEYALYPTLTAYENLMYFGSLYNVSKADLKAKIPEFLIHL 124

Query: 122 QLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKE 181
            L  ++ +  +  SGG ++RV +   I+ +PKV   DEP   +D   R AT ++  +L  
Sbjct: 125 GLENFMHKKIQTFSGGMKRRVNLIAGILHNPKVLFLDEPTVGVDVQSR-ATIIDYLKLLN 183

Query: 182 AMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPEN 228
               +T+VY +H   EA    T I ++  G +   G+P EL E   N
Sbjct: 184 -QQGTTIVYTSHLMAEAQDFCTDIAIIDQGSVFVQGTPKELIENVPN 229


Lambda     K      H
   0.316    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: 186
Number of extensions: 14
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: 373
Length of database: 249
Length adjustment: 27
Effective length of query: 346
Effective length of database: 222
Effective search space:    76812
Effective search space used:    76812
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: 48 (23.1 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