GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Hydrogenovibrio kuenenii DSM 12350

Align TreV, component of Trehalose porter (characterized)
to candidate WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>NCBI__GCF_000526715.1:WP_024852149.1
          Length = 263

 Score =  147 bits (372), Expect = 2e-40
 Identities = 93/233 (39%), Positives = 135/233 (57%), Gaps = 6/233 (2%)

Query: 3   VELIDIVKKYGKNI--VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKII 60
           V + ++   Y K +  V+  I   I  G+   ++G SG GKSTLL+++AG+     G + 
Sbjct: 8   VWIAELSHSYKKQLPPVLTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGVVR 67

Query: 61  ADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLL 120
            +G  +  KP  K N  M+FQ  +LYP MSVR+N A  L   G  K++  +RVE+   ++
Sbjct: 68  INGKTVV-KPSAKWN--MMFQKPSLYPWMSVRENAALGLVFAGTYKQKQ-DRVEELLDMV 123

Query: 121 GISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQK 180
           G+SE  DK V ++SGGQQQRVALAR++   P   LLDEP S LDA  RT  + E+ +I  
Sbjct: 124 GLSEHKDKNVQELSGGQQQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQICH 183

Query: 181 ELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFV 233
           E   T I VTHD +EA+++AD++ I+     E V D      YP+ +  A F+
Sbjct: 184 EQGITMIMVTHDIEEAIAMADKVVIMSHNPGEIVGDLDVPLTYPRDRSAADFI 236


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: 207
Number of extensions: 8
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: 263
Length adjustment: 26
Effective length of query: 298
Effective length of database: 237
Effective search space:    70626
Effective search space used:    70626
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 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