GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Shewanella amazonensis SB2B

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 6938989 Sama_3087 ABC transporter, ATP-binding protein (RefSeq)

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__SB2B:6938989
          Length = 243

 Score =  148 bits (374), Expect = 9e-41
 Identities = 80/250 (32%), Positives = 140/250 (56%), Gaps = 14/250 (5%)

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

Query: 67  ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKG 126
            +         +H  A+ GI    Q   +F +++  +N+M    +R            K 
Sbjct: 63  HINDDDLTLDPMHLRARKGIGYLPQEASIFRKLSVRDNIMAVLQMR------------KE 110

Query: 127 FKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAA 186
              +E   A   ++LL+   I    D    +LS G++RR+EIARALA +P+ I LDEP A
Sbjct: 111 LNTDEREEA--LEQLLEEFHITHIRDNLGMSLSGGERRRVEIARALAANPRFILLDEPFA 168

Query: 187 GMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQK 246
           G++    + ++++I++++N    +L+ +H+V+  + +C++  ++ +G  IAEG PAE+  
Sbjct: 169 GVDPISVIDIKKIIEQLKNRGLGVLITDHNVRETLDVCEKAYIVSHGDLIAEGTPAEILD 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: 156
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