GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Malonomonas rubra DSM 5091

Align TreV, component of Trehalose porter (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= TCDB::Q97ZC0
         (324 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  149 bits (376), Expect = 1e-40
 Identities = 85/241 (35%), Positives = 139/241 (57%), Gaps = 7/241 (2%)

Query: 8   IVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADIT 67
           I +K    + +   + +I  GE FVI+G SG GKST++++L  + +   G+++ DG DI 
Sbjct: 36  IFEKTETTVGVQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIV 95

Query: 68  DKPPE------KRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLG 121
               +      +  ++MVFQ++AL P+M+V  N AF L+M G+ K+   +R  +A + +G
Sbjct: 96  AMNDDQLVKVRRAKLSMVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVG 155

Query: 122 ISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKE 181
           +    +    ++SGG QQRV LAR +  +P   L+DE  S LD  +RT  + EL ++Q +
Sbjct: 156 LEAWAESMPDELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAK 215

Query: 182 LKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWV-AQFVGEFPMNF 240
            K T ++++HD  EA+ + DRIAI+  G+  QV  P+ + + P   +V A F G  P N 
Sbjct: 216 AKRTIVFISHDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRGVDPTNI 275

Query: 241 L 241
           L
Sbjct: 276 L 276


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: 286
Number of extensions: 7
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: 415
Length adjustment: 30
Effective length of query: 294
Effective length of database: 385
Effective search space:   113190
Effective search space used:   113190
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 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