GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Flavobacterium beibuense F44-8

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_035136158.1 Q763_RS16555 ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc03065
         (362 letters)



>NCBI__GCF_000769915.1:WP_035136158.1
          Length = 234

 Score =  114 bits (284), Expect = 3e-30
 Identities = 68/215 (31%), Positives = 110/215 (51%), Gaps = 9/215 (4%)

Query: 5   LLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDG 64
           L K  R        ++ I +++K+GEFV  +G SGCGKSTLL ++  L+  +GG   +  
Sbjct: 7   LSKVFRTEEVETKALNDISIEVKKGEFVTIMGASGCGKSTLLNIVGLLDSASGGSYKLLD 66

Query: 65  ERVNDVPPS------KRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAA 118
             +N +  S      K  I  VFQ++ L   ++VYDN+   +        E  +RV   A
Sbjct: 67  REINGLSESEKAKVRKENIGFVFQNFNLIDELSVYDNIELPLIYNNVPSGERKKRVEEIA 126

Query: 119 DMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAK 178
           + L ++  L   P+ LSGGQ+QR A+ RA+  NPK+ L DEP  NLD+  +    +    
Sbjct: 127 ERLGISHRLKHYPQQLSGGQQQRAAVARALVNNPKIILADEPTGNLDS--KNGNEVMELL 184

Query: 179 LSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHI 213
                +  T++ VTH + +A + + + + +  G I
Sbjct: 185 TDLHANGATILMVTHSEYDA-SFSQKTIYMKDGMI 218


Lambda     K      H
   0.320    0.137    0.387 

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: 200
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: 362
Length of database: 234
Length adjustment: 26
Effective length of query: 336
Effective length of database: 208
Effective search space:    69888
Effective search space used:    69888
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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