GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Malonomonas rubra DSM 5091

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

Query= uniprot:Q6MNM2
         (347 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  152 bits (385), Expect = 1e-41
 Identities = 82/215 (38%), Positives = 130/215 (60%), Gaps = 6/215 (2%)

Query: 25  DIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGKKI---ND---IEPQNRDIA 78
           +I  GE  V++G SG GKST++R L  L    SG + IDG+ I   ND   ++ +   ++
Sbjct: 52  EIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKVRRAKLS 111

Query: 79  MVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQIKHLLDRKPKELSGGQ 138
           MVFQS+AL PHMTV +N  FGL++  +      +R  +  E + ++   +  P ELSGG 
Sbjct: 112 MVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPDELSGGM 171

Query: 139 RQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKSTMIYVTHDQMEAT 198
           +QRV L R L+    ++L DE  S LD  +R++M+ E+ +L   +K T+++++HD  EA 
Sbjct: 172 QQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISHDLDEAM 231

Query: 199 TLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATF 233
            +GDRIA+++ G + Q+GTP EI   P + ++  F
Sbjct: 232 RIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAF 266


Lambda     K      H
   0.318    0.136    0.383 

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: 315
Number of extensions: 11
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: 347
Length of database: 415
Length adjustment: 30
Effective length of query: 317
Effective length of database: 385
Effective search space:   122045
Effective search space used:   122045
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: 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