GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Malonomonas rubra DSM 5091

Align ATPase (characterized, see rationale)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= uniprot:Q31RN8
         (261 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  137 bits (344), Expect = 5e-37
 Identities = 82/218 (37%), Positives = 122/218 (55%), Gaps = 4/218 (1%)

Query: 42  SLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRL--SHDRRDIATIRQE 99
           S  + +GE+ V+MG SGSGKST +R LN L     G++ I+G  +   +D + +   R +
Sbjct: 50  SFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKVRRAK 109

Query: 100 VGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQADKYPGQLS 159
           + MVFQ F L PH+TVLQN     +++        E  A Q LE+V +   A+  P +LS
Sbjct: 110 LSMVFQSFALMPHMTVLQNAAFG-LEMDGVDKQTREQRALQALEQVGLEAWAESMPDELS 168

Query: 160 GGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDL-ASEGMTMLVATHEVG 218
           GG QQRV +AR LA+ P ILL DE  SALDP +  E+ D +  L A    T++  +H++ 
Sbjct: 169 GGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISHDLD 228

Query: 219 FAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQF 256
            A  + DR+ +M  G++V+   P+     P  D  + F
Sbjct: 229 EAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAF 266


Lambda     K      H
   0.321    0.134    0.387 

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: 230
Number of extensions: 9
Number of successful extensions: 4
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: 261
Length of database: 415
Length adjustment: 28
Effective length of query: 233
Effective length of database: 387
Effective search space:    90171
Effective search space used:    90171
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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