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 GFF2754 PGA1_c27970 ATP-binding transport protein SmoK

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__Phaeo:GFF2754
          Length = 331

 Score =  307 bits (787), Expect = 2e-88
 Identities = 177/357 (49%), Positives = 227/357 (63%), Gaps = 32/357 (8%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           M  L+LT V K++G V+VL +INL ++ GE +VFVGPSGCGKSTLLR+I+GLE  T G +
Sbjct: 1   MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60

Query: 61  EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120
            I G  V   PPA+RGIAMVFQSYALYPH++VRENM+ ALK  ++ + EI A V  A+  
Sbjct: 61  SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120

Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180
           L L  YLDR P  LSGGQRQRVAIGR++VR+PK++LFDEPLSNLDAALR+ TRLEIA+L 
Sbjct: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180

Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240
             +  ++M+YVTHDQ+EAMTLA +IVVL  G I QVG+P+ELY  P N FVA+FIG+P M
Sbjct: 181 RQL-SASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAM 239

Query: 241 NLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVFE 300
           N +P + +G                               +G+RPE     +P G     
Sbjct: 240 NFVPAQRLGG-------------------------NPGQFIGIRPE-YARISPVGP--LA 271

Query: 301 GKVAITEALGEVTLLYFEAPSGEDPTI-GKLQGIHKDLKGQVTRLTAEPAKVHVFKD 356
           G+V   E LG  T +  +   GED T   +L G H    G+  +   +PA    F +
Sbjct: 272 GEVIHVEKLGGDTNILVD--MGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDE 326


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: 380
Number of extensions: 15
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: 373
Length of database: 331
Length adjustment: 29
Effective length of query: 344
Effective length of database: 302
Effective search space:   103888
Effective search space used:   103888
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