GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Hydrogenovibrio kuenenii DSM 12350

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_000526715.1:WP_024851725.1
          Length = 282

 Score =  148 bits (373), Expect = 2e-40
 Identities = 93/215 (43%), Positives = 131/215 (60%), Gaps = 15/215 (6%)

Query: 6   LTGVEKAY----GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLE 61
           ++G+ K +    G V+VL +I+L +++ E +  VG SGCGKSTLLR+I GLEK+T G + 
Sbjct: 7   ISGLNKTFITKKGAVEVLESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTKGQVL 66

Query: 62  IDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQ----AEIDAAVE-- 115
           +D  +VN  P   R  AMVFQ Y+LYP +TV+EN+ F+  +    Q     +I + V+  
Sbjct: 67  VDEEIVNK-PGKDR--AMVFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSMVDRS 123

Query: 116 -AAAEKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRL 174
            A  + + L +  D  P  LSGG RQRVAI R+++  P V L DEP   LDA  R     
Sbjct: 124 YALLDLMGLEKVQDSHPNQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTREVMHD 183

Query: 175 EIAQLKEAMPESTMVYVTHDQVEAMTLATRIVVLA 209
            I  L E + +ST+V+VTHD  EA+ LA R+VV+A
Sbjct: 184 LILHLFE-IEKSTIVFVTHDVEEAIYLADRVVVMA 217


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: 266
Number of extensions: 16
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: 282
Length adjustment: 28
Effective length of query: 345
Effective length of database: 254
Effective search space:    87630
Effective search space used:    87630
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 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