GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Desulfacinum hydrothermale DSM 13146

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_084058302.1 B9A12_RS12460 ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_900176285.1:WP_084058302.1
          Length = 361

 Score =  174 bits (442), Expect = 3e-48
 Identities = 106/284 (37%), Positives = 161/284 (56%), Gaps = 10/284 (3%)

Query: 19  LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVNDVPPAQRGIA 78
           L NI+   + G     +GPSGCGK+T+L +I+GL   T G +  D   V ++PP QR IA
Sbjct: 25  LKNIDTVWEDGGAYALLGPSGCGKTTMLNIISGLLTPTRGRVLYDDRDVTELPPEQRNIA 84

Query: 79  MVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKALSGGQ 138
            VFQ   LY  M+V +N++F L+        I   V+  AE L L   L +    LS   
Sbjct: 85  QVFQFPVLYDTMSVFDNLAFPLRNRGLDPQTIHRRVQEVAEVLDLTADLKKKAAGLSADA 144

Query: 139 RQRVAIGRSIVR-DPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTHDQVE 197
           +Q++++GR +VR D    LFDEPL+ +D  L+   R ++ ++ E + + T++YVTHDQVE
Sbjct: 145 KQKISLGRGLVREDVAAILFDEPLTVIDPHLKWHLRRKLKEIHEKL-QLTLIYVTHDQVE 203

Query: 198 AMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGKIIGTGAQTTVE 257
           A+T A +++V+  G + Q+G+P EL+E+P ++FV  FIGSP MN +P ++ G  A     
Sbjct: 204 ALTFADKVLVMYEGEMVQMGTPAELFEEPRHKFVGYFIGSPGMNFIPCRLEGNRA----- 258

Query: 258 MTDGGRAVSDYPSDDSLMG--AAVNVGVRPEDM-VEAAPGGDYV 298
           + DG   V D  +     G      +G+RP  + V   PG D +
Sbjct: 259 VCDGASVVLDEETVRRAQGKEGPFELGIRPMYLEVHDEPGDDRI 302


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: 344
Number of extensions: 17
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: 373
Length of database: 361
Length adjustment: 30
Effective length of query: 343
Effective length of database: 331
Effective search space:   113533
Effective search space used:   113533
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