GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Desulfovibrio vulgaris Hildenborough

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 209035 DVU0105 glutamine ABC transporter, ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>MicrobesOnline__882:209035
          Length = 244

 Score =  162 bits (409), Expect = 1e-44
 Identities = 97/238 (40%), Positives = 141/238 (59%), Gaps = 7/238 (2%)

Query: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63
           +++  + K+YGD  VL  I+L ++ GE++V +GPSG GKST LR I  LE+IT GT+ +D
Sbjct: 5   IEIRNLHKSYGDHHVLRGIDLTVRTGEVVVVIGPSGSGKSTALRCINRLEEITSGTIIVD 64

Query: 64  GTVV----NDVPPAQRGIAMVFQSYALYPHMTVRENMSFA-LKIAKKSQAEIDAAVEAAA 118
           G  +     D+   +    MVFQ + L+PHM+V EN++   +K+ + ++ E  A   A  
Sbjct: 65  GYDLYDPKTDINHVRTEAGMVFQQFNLFPHMSVLENVTIGPVKVRRMARQEAQALGLALL 124

Query: 119 EKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQ 178
           EK+ L       P  LSGGQ+QRVAI RS+   PKV LFDEP S LD  L V   LE+ +
Sbjct: 125 EKVGLADKAHAYPDQLSGGQKQRVAIARSLAMQPKVLLFDEPTSALDPEL-VGEVLEVMK 183

Query: 179 LKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIG 236
            + A    TMV VTH+   A  +A R++ +  G I + G P EL+  P+N  + +F+G
Sbjct: 184 -QLAREGMTMVVVTHEMGFAREVADRVIFIDYGKIQEEGPPNELFADPKNPRLREFLG 240


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: 247
Number of extensions: 12
Number of successful extensions: 4
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: 244
Length adjustment: 27
Effective length of query: 346
Effective length of database: 217
Effective search space:    75082
Effective search space used:    75082
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 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