GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Shewanella amazonensis SB2B

Align TreV, component of Trehalose porter (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__SB2B:6938538
          Length = 378

 Score =  202 bits (513), Expect = 1e-56
 Identities = 102/233 (43%), Positives = 157/233 (67%), Gaps = 2/233 (0%)

Query: 18  INGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKPPEKRNVA 77
           ++ ++  I  GE F +LG SG GKSTLL++LAG E+  +G+I  DG DITD PP +R + 
Sbjct: 36  VDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYLDGQDITDLPPYERPIN 95

Query: 78  MVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKVTQISGGQ 137
           M+FQ+YAL+P+M+V  NIAF LK   M K +I +RV++  KL+ + +   +K  Q+SGGQ
Sbjct: 96  MMFQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEMLKLVHMEQYAKRKPHQLSGGQ 155

Query: 138 QQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVTHDQKEAL 197
           +QRVALAR++ + P   LLDEP+  LD ++RT  + E+  I + +  T + VTHDQ+EA+
Sbjct: 156 RQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAM 215

Query: 198 SLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLPGELMKEKA 250
           ++A RIAI+  G   QV  P  +YE P ++ +A+F+G   +N    E+++++A
Sbjct: 216 TMAGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFIG--TVNLFDCEIIEDEA 266


Lambda     K      H
   0.318    0.137    0.385 

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: 291
Number of extensions: 10
Number of successful extensions: 1
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: 324
Length of database: 378
Length adjustment: 29
Effective length of query: 295
Effective length of database: 349
Effective search space:   102955
Effective search space used:   102955
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 (21.7 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