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 GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__Phaeo:GFF1645
          Length = 355

 Score =  343 bits (881), Expect = 3e-99
 Identities = 199/361 (55%), Positives = 243/361 (67%), Gaps = 11/361 (3%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           MA ++L  V K YG V+VL +INLDIQ GE IV VGPSGCGKSTLLRMIAGLE IT G  
Sbjct: 1   MARIELRDVAKRYGAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPITSGDF 60

Query: 61  EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120
           EIDG  +NDV P  R IAMVFQSYALYPHM V  NM F+++I K    E  + V  AAE 
Sbjct: 61  EIDGQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKDPAEERRSRVARAAET 120

Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180
           L L   +DRLPKALSGGQRQRVA+GR+I+RDP+ +LFDEPLSNLDAALRV  RLEIA+L 
Sbjct: 121 LGLSSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRLEIARLH 180

Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240
           + +  +TM+YVTHDQVEA+TLA RIVVL GG I QVGSPLELYE+P N+FVAQFIGSP M
Sbjct: 181 KQL-GATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFIGSPTM 239

Query: 241 NLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVFE 300
           N+LP     +GA + V  T+G     D+  D +   AAV +G+RPE +    PG  ++  
Sbjct: 240 NILP----VSGAASGVMATNGMMLTLDHMHDTA---AAVELGIRPEHLDVVEPGEGHLI- 291

Query: 301 GKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVFKD-GVS 359
               + E LG  T +Y +   G  P + +  G      G+   L  +    H+F D G++
Sbjct: 292 AVADVVERLGSDTNIYAKV-DGLGPLMVRKHGNVPVRSGERLGLRVQAQNAHIFDDRGIA 350

Query: 360 L 360
           L
Sbjct: 351 L 351


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: 389
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: 373
Length of database: 355
Length adjustment: 29
Effective length of query: 344
Effective length of database: 326
Effective search space:   112144
Effective search space used:   112144
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