GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Dyella japonica UNC79MFTsu3.2

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein

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



>FitnessBrowser__Dyella79:N515DRAFT_4212
          Length = 364

 Score =  298 bits (763), Expect = 2e-85
 Identities = 171/367 (46%), Positives = 232/367 (63%), Gaps = 11/367 (2%)

Query: 1   MTGLLLKDIRKSY--GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGG 58
           M  + L  +RK Y  G V V      +I +GE +V VGPSGCGK+TLLRMIAGLE I+GG
Sbjct: 1   MAKVRLDKLRKVYPNGHVGVAEA-SFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGG 59

Query: 59  DMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAA 118
            + I    VND+ P  R IAMVFQ+YALYPHMTV +N+ FG+++  + K EI+RRV  AA
Sbjct: 60  TLSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAA 119

Query: 119 DMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAK 178
            ML+L   LD  P ALSGGQRQRVA+GRA+ R+PKVFL DEPLSNLDA LR++ R+EIA+
Sbjct: 120 RMLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIAR 179

Query: 179 LSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSP 238
           + +R+   TM+YVTHDQ+EAMTL  RIVVL+ G I+Q+  P+ LY+ PANLFVA F+GSP
Sbjct: 180 IHQRLK-ATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSP 238

Query: 239 AMNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENG---KTASFGVRPEDLRV-TEAD 294
           AMN++   +   G    +++  G+ V  ++P  A+      +    G+RPEDL +  +A 
Sbjct: 239 AMNLLRGILYRDG-GWKLAMPQGELVLGELPQGAALEAWRDRDIVVGLRPEDLLLCADAA 297

Query: 295 DFLFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFD 354
                  + +VE +G    L +        ++++MP       G  + F     +LH FD
Sbjct: 298 GAALAAQLEVVEPVGNEVFLNLRH--GELALVSRMPPRELPAPGSTLHFGFAPERLHFFD 355

Query: 355 TNGQSYR 361
             G+  R
Sbjct: 356 AKGEGAR 362


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: 369
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: 362
Length of database: 364
Length adjustment: 29
Effective length of query: 333
Effective length of database: 335
Effective search space:   111555
Effective search space used:   111555
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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