GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Shewanella sp. ANA-3

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 7023443 Shewana3_0673 ABC transporter related (RefSeq)

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__ANA3:7023443
          Length = 243

 Score =  149 bits (376), Expect = 5e-41
 Identities = 81/250 (32%), Positives = 139/250 (55%), Gaps = 14/250 (5%)

Query: 7   EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66
           ++ LK   ++K +   Q + DV +T+K GQV GL+GPNGAGKTT F ++ GL   D G  
Sbjct: 3   QITLKAQNLAKSYKSRQVVKDVSLTVKTGQVVGLLGPNGAGKTTTFYMVVGLVKSDKGHI 62

Query: 67  ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKG 126
            +         +H  A+ GI    Q   +F ++T  +N+M             AV +T+ 
Sbjct: 63  FIDDDDLTADPMHLRARKGIGYLPQEASIFRKLTVHDNIM-------------AVLQTRK 109

Query: 127 FKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAA 186
            +       +  + LL+   I    D +  +LS G++RR+EIARALA +P+ I LDEP A
Sbjct: 110 -ELNRDQREEELEHLLEEFHITHIRDSQGMSLSGGERRRVEIARALAANPKFILLDEPFA 168

Query: 187 GMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQK 246
           G++    + ++++I+++++    +L+ +H+V+  + +C+   ++ +G  IAEG PAE+  
Sbjct: 169 GVDPISVIDIKKIIEQLKSRGLGVLITDHNVRETLDVCEHAYIVSHGNLIAEGTPAEILD 228

Query: 247 NEKVIEAYLG 256
           N++V   YLG
Sbjct: 229 NQQVRAVYLG 238


Lambda     K      H
   0.319    0.137    0.384 

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: 161
Number of extensions: 8
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: 260
Length of database: 243
Length adjustment: 24
Effective length of query: 236
Effective length of database: 219
Effective search space:    51684
Effective search space used:    51684
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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