GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aglK in Phaeobacter inhibens BS107

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate GFF776 PGA1_c07900 alpha-glucoside transport ATP-binding protein AglK

Query= uniprot:A8LLL2
         (373 letters)



>lcl|FitnessBrowser__Phaeo:GFF776 PGA1_c07900 alpha-glucoside
           transport ATP-binding protein AglK
          Length = 363

 Score =  520 bits (1338), Expect = e-152
 Identities = 267/363 (73%), Positives = 310/363 (85%), Gaps = 2/363 (0%)

Query: 1   MADLKLTGVEKAYGD-VKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59
           MA+LKLT V K YG  V+VL +INLDI+QGELIVFVGPSGCGKSTLLRMIAGLE+I+GGT
Sbjct: 1   MANLKLTNVAKTYGGGVEVLRDINLDIKQGELIVFVGPSGCGKSTLLRMIAGLERISGGT 60

Query: 60  LEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119
           LEID  V+ND+PPAQRGIAMVFQSYALYPHMTVR+NM+FALKIAKKS+ EIDAA++ AA+
Sbjct: 61  LEIDNAVMNDIPPAQRGIAMVFQSYALYPHMTVRDNMAFALKIAKKSKDEIDAAIDRAAK 120

Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179
            LQL  YLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATR+EIAQL
Sbjct: 121 ILQLEPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQL 180

Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPK 239
           KEAMP+STM+YVTHDQVEAMTLA+RIVVLA  GIAQVG+PL+LY++PENEFVAQFIGSP 
Sbjct: 181 KEAMPDSTMIYVTHDQVEAMTLASRIVVLADKGIAQVGTPLDLYQRPENEFVAQFIGSPA 240

Query: 240 MNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVF 299
           MNL+PG ++ TG +TTV +T G   V++ P+ D+  G AVNVGVRPED+VE   GG  + 
Sbjct: 241 MNLIPGTVVATGPRTTVRLTSGEEVVAEIPTTDADQGLAVNVGVRPEDLVEEGTGGALI- 299

Query: 300 EGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVFKDGVS 359
           + +V I EALGEVT+LY  A  G+DP I KL GIHK L+G   RL A+PA++H+F +G S
Sbjct: 300 DSRVDIVEALGEVTVLYIAAGEGKDPLIAKLPGIHKGLRGSSVRLYADPARLHLFHNGQS 359

Query: 360 LHY 362
           L Y
Sbjct: 360 LLY 362


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: 499
Number of extensions: 22
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: 363
Length adjustment: 30
Effective length of query: 343
Effective length of database: 333
Effective search space:   114219
Effective search space used:   114219
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