GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF776
          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:

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