GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Desulfoscipio geothermicus DSM 3669

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_900115975.1:WP_092484009.1
          Length = 344

 Score =  175 bits (444), Expect = 1e-48
 Identities = 108/308 (35%), Positives = 172/308 (55%), Gaps = 25/308 (8%)

Query: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63
           L+L  V    G+ ++L +INL++Q+GE  + +GP+G GK+ +L  IAG+ +   GT+   
Sbjct: 2   LRLEHVTVKLGEFQLL-DINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFK 60

Query: 64  GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123
              +  + P QR +  V+Q YAL+PH+TV+EN+ F  +I K  +  I + ++     L +
Sbjct: 61  ERNLATLAPEQRKVGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGI 120

Query: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183
           G  L+R P  LSGG++QR A+ R+++  P++ L DEPLS LD   +   + E+ ++ + +
Sbjct: 121 GHLLNRHPSTLSGGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTL 180

Query: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243
            ++T ++VTHD  EAM LA +I V+  G I QVG+P E++ KP+N+FVA F+G    N+ 
Sbjct: 181 -KTTTLHVTHDFNEAMYLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVGIE--NIF 237

Query: 244 PGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAA----VNVGVRPEDMVEAAPGGD--- 296
            G++                 VS  P  D  +       V V V PED+  +    D   
Sbjct: 238 EGQV-------------NDDKVSLAPDVDIFVNTGKQGKVKVAVPPEDIALSKEPFDLCY 284

Query: 297 -YVFEGKV 303
            Y F GKV
Sbjct: 285 HYQFNGKV 292


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: 312
Number of extensions: 19
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: 344
Length adjustment: 29
Effective length of query: 344
Effective length of database: 315
Effective search space:   108360
Effective search space used:   108360
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: 49 (23.5 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