GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Erythrobacter gangjinensis K7-2

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_047006469.1 AAW01_RS01810 phosphate ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_001010925.1:WP_047006469.1
          Length = 280

 Score =  104 bits (259), Expect = 3e-27
 Identities = 74/247 (29%), Positives = 125/247 (50%), Gaps = 19/247 (7%)

Query: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKI-----TGG 58
           ++  GV+  YGD + + ++++DI    +  F+GPSGCGKST LR +  +          G
Sbjct: 33  MRAQGVDVYYGDKRAIDDVSIDIYTEYVTAFIGPSGCGKSTFLRALNRMNDTIPSASVKG 92

Query: 59  TLEIDGTVV----NDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKI--AKKSQAEIDA 112
            +E+DG  +     DV   +  + MVFQ    +P  ++ EN+++  +I    +++ ++D 
Sbjct: 93  RIELDGDDIYASGMDVVQLRARVGMVFQKPNPFP-KSIYENIAYGPRIHGLAENRNDVDE 151

Query: 113 AVEAAAEKLQLGQYL-DRLP---KALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAAL 168
            VE +  +  L + + DRL     ALSGGQ+QR+ I R+I  DP+V L DEP S LD   
Sbjct: 152 IVEKSLRRAGLWEEVKDRLQDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDP-- 209

Query: 169 RVATRLEIAQLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPEN 228
            +AT      + E      +V VTH   +A  ++ R      G + + G   +++  P  
Sbjct: 210 -IATAKIEELIDELRGRYGIVIVTHSMQQAARVSQRTAFFHLGKMVEYGHTSDIFTNPRE 268

Query: 229 EFVAQFI 235
           +    +I
Sbjct: 269 KRTQDYI 275


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: 205
Number of extensions: 11
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: 280
Length adjustment: 28
Effective length of query: 345
Effective length of database: 252
Effective search space:    86940
Effective search space used:    86940
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 24 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