GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aglK' in Burkholderia phytofirmans PsJN

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate BPHYT_RS16095 BPHYT_RS16095 sugar ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS16095 BPHYT_RS16095 sugar ABC
           transporter ATP-binding protein
          Length = 369

 Score =  343 bits (879), Expect = 6e-99
 Identities = 192/356 (53%), Positives = 235/356 (66%), Gaps = 6/356 (1%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           MA + L  + KAY + +V+ +INLDI  GE +VFVGPSGCGKSTL+RMIAGLE I+GG L
Sbjct: 1   MASVTLRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDL 60

Query: 61  EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120
            IDG  VNDV PA+RGIAMVFQSYALYPHMT+ +NM+F LK+A   + EIDAAV  AA+ 
Sbjct: 61  TIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKI 120

Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180
           L +   LDR PK LSGGQRQRVAIGR+I R PKV+LFDEPLSNLDAALRV  RLE A+L 
Sbjct: 121 LHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLH 180

Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240
           + + ++TM+YVTHDQVEAMTLA +IVVL+ G + QVGSP  LY  P N FVA FIGSPKM
Sbjct: 181 DEL-KTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKM 239

Query: 241 NLLPGKIIG-TGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDM-VEAAPGGDYV 298
           N + G +   T    TV    G              G  V VG+RPE + V  A  G   
Sbjct: 240 NFMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVGMAEDG--- 296

Query: 299 FEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354
              +    E+LG+   LY E+    D  I ++  + +  KG+  +L A P   H+F
Sbjct: 297 ISARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATPEHCHLF 352


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: 432
Number of extensions: 24
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: 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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