GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Shewanella loihica PV-4

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__PV4:5208351
          Length = 342

 Score =  176 bits (447), Expect = 6e-49
 Identities = 122/359 (33%), Positives = 191/359 (53%), Gaps = 22/359 (6%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           M+ L +  V   Y    +L  ++L + QGE+   +GPSGCGK+TLL+ IAGL+ I+ G +
Sbjct: 1   MSTLTIEQVHSDYQGQTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRI 60

Query: 61  EIDGTVVND----VPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEA 116
            I+G +++     VP  +R + M+FQ YAL+PH+TV EN+ F +K   K+  +       
Sbjct: 61  SINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVKGLDKAARQARLGEML 120

Query: 117 AAEKLQ-LGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLE 175
           A  KL+ LG    R P  LSGGQ+QRV+I R++  +P++ L DEP SN+DA +R    +E
Sbjct: 121 ALVKLEGLG---GRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVE 177

Query: 176 IAQLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFI 235
           I ++ +    S  V+VTH + EA   A ++ +   GGIAQ GS   LY +P +++VA+F+
Sbjct: 178 IREILKQRGVSA-VFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFL 236

Query: 236 GSPKMNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGG 295
           G  ++N L  ++       T  +    ++ SD P      G  +   +RPE +  A   G
Sbjct: 237 G--QVNYLSCEVKDRARLQT--LLGEVQSSSDLPKAAGYRGELL---LRPEQLQMA---G 286

Query: 296 DYVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354
           D   EG +     LG   L ++    GE+  +     +H    GQ   L+  P    +F
Sbjct: 287 DEQGEGTIIARRFLG--NLCHYSILIGEE-ILAVRSPLHHFSPGQKVGLSVTPHPAVLF 342


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: 339
Number of extensions: 15
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: 342
Length adjustment: 29
Effective length of query: 344
Effective length of database: 313
Effective search space:   107672
Effective search space used:   107672
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