GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Rhizorhabdus wittichii RW1

Align TreV, component of Trehalose porter (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  136 bits (343), Expect = 5e-37
 Identities = 73/214 (34%), Positives = 121/214 (56%), Gaps = 3/214 (1%)

Query: 10  KKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDK 69
           K Y    V++ ++  IE G F  ++G SG GK+TLLK +  + ++D G I  +G D+  +
Sbjct: 9   KHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIEGRDVAAQ 68

Query: 70  PPE--KRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI-SEIL 126
           P    +R +  VFQ   L+P+MSV +N+A   +++G+ +EE   RV +   L+ + ++  
Sbjct: 69  PVAELRRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLDLVALPADFA 128

Query: 127 DKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTF 186
           +++  Q+SGGQ QRV  ARA+   P+  L+DEP   LD   R       + + + +  T 
Sbjct: 129 ERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALHEAMGLTS 188

Query: 187 IYVTHDQKEALSLADRIAILHKGKFEQVSDPKTL 220
           + VTHD  EAL LADR+ ++ +G+      P+ L
Sbjct: 189 LIVTHDMAEALLLADRVIVIGEGRILADQPPRAL 222


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: 169
Number of extensions: 7
Number of successful extensions: 3
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: 252
Length adjustment: 26
Effective length of query: 298
Effective length of database: 226
Effective search space:    67348
Effective search space used:    67348
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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