GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Thiothrix lacustris DSM 21227

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  216 bits (551), Expect = 6e-61
 Identities = 123/286 (43%), Positives = 178/286 (62%), Gaps = 5/286 (1%)

Query: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63
           L L+ + K +   +VLS+ NL IQ GE    +GPSGCGK+T+LR+IAG E+   G + ++
Sbjct: 7   LTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLN 66

Query: 64  GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123
           G  +  +P  +R    VFQSYAL+PH+TV +N++F LK+A     +I   V  A   ++L
Sbjct: 67  GDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRL 126

Query: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183
            ++  R P  LSGGQ+QRVAI R++V  PK+ L DE LS LD  LR   +LE+ QL+  +
Sbjct: 127 SEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQL 186

Query: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243
              T VYVTHDQ EA++++ RI+V+  G   QVG+P E+YE P N FVAQFIG  ++N+ 
Sbjct: 187 -GITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIG--EINVF 243

Query: 244 PGKIIGTGAQTTVEMTDGGRAVSDYPSDDSL-MGAAVNVGVRPEDM 288
            G+I+    +   E +  G  V +   D    +G  V+V +RPED+
Sbjct: 244 DGEIVQALGEYQYEASING-VVREIRCDHRFAVGDKVHVMLRPEDL 288


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: 336
Number of extensions: 17
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: 369
Length adjustment: 30
Effective length of query: 343
Effective length of database: 339
Effective search space:   116277
Effective search space used:   116277
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