GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Dechlorosoma suillum PS

Align TreV, component of Trehalose porter (characterized)
to candidate Dsui_1462 Dsui_1462 ABC-type antimicrobial peptide transport system, ATPase component

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__PS:Dsui_1462
          Length = 267

 Score =  136 bits (343), Expect = 5e-37
 Identities = 77/200 (38%), Positives = 115/200 (57%), Gaps = 7/200 (3%)

Query: 17  VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKPPEK--- 73
           V+  I+  I  GEF  ++GPSG GKSTLL ++AGI++ D G +   G DI      +   
Sbjct: 59  VLERISFNIAAGEFLALMGPSGSGKSTLLNLIAGIDRPDSGTLSVAGQDIAALEEAELAA 118

Query: 74  ---RNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKV 130
               NV  +FQ Y L P ++  +N+  PL ++ + K E  ER E A  ++G+++ +D   
Sbjct: 119 WRAENVGFIFQFYNLMPVLTALENVELPLLLKNLGKAERRERAELALSMVGLADRMDHTP 178

Query: 131 TQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVT 190
            ++SGGQQQRVA+ARA++ +P+  + DEP  +LD          L+R+  EL  T + VT
Sbjct: 179 NELSGGQQQRVAIARALITDPTLIVADEPTGDLDRESAGDILHLLQRLNDELGKTIVMVT 238

Query: 191 HDQKEALSLADRIAILHKGK 210
           HDQ+ A S A  I  L KG+
Sbjct: 239 HDQRAAES-AHAIMHLEKGE 257


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: 204
Number of extensions: 11
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: 324
Length of database: 267
Length adjustment: 26
Effective length of query: 298
Effective length of database: 241
Effective search space:    71818
Effective search space used:    71818
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: 48 (23.1 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