GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Malonomonas rubra DSM 5091

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  169 bits (429), Expect = 1e-46
 Identities = 98/228 (42%), Positives = 133/228 (58%), Gaps = 13/228 (5%)

Query: 16  TVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMNYRVPQNR 75
           TV V D S +I   E  V++G SG GKST +RML  L  PTSG + I G+ +   V  N 
Sbjct: 43  TVGVQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDI---VAMND 99

Query: 76  D---------IAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIAD 126
           D         ++MVFQ +AL PHMTV QN  FGLE + G     R++R ++  E +G+  
Sbjct: 100 DQLVKVRRAKLSMVFQSFALMPHMTVLQNAAFGLEMD-GVDKQTREQRALQALEQVGLEA 158

Query: 127 LLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAV 186
             +  PDELSGG QQRV L R +  DP++ LMDE  S LD  +R EM+ EL  LQ +   
Sbjct: 159 WAESMPDELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKR 218

Query: 187 TTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEF 234
           T V+++H+  EAM + DRIA+M+ G + QV +P E    P + +V  F
Sbjct: 219 TIVFISHDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAF 266


Lambda     K      H
   0.317    0.135    0.386 

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: 385
Number of extensions: 32
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: 383
Length of database: 415
Length adjustment: 31
Effective length of query: 352
Effective length of database: 384
Effective search space:   135168
Effective search space used:   135168
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 (21.6 bits)
S2: 50 (23.9 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