GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Malonomonas rubra DSM 5091

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= reanno::Smeli:SMc02869
         (352 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  155 bits (392), Expect = 2e-42
 Identities = 86/240 (35%), Positives = 133/240 (55%), Gaps = 7/240 (2%)

Query: 41  DVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQIDGVEV-----GHVAPAKRG-IA 94
           ++  GE  + +G SG GKST++R +  L + TSG V IDG ++       +   +R  ++
Sbjct: 52  EIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKVRRAKLS 111

Query: 95  MVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSLEPYLARRPAELSGGQ 154
           MVFQS+AL PH+TV  N   GL+  GV K   E++  +A   + LE +    P ELSGG 
Sbjct: 112 MVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPDELSGGM 171

Query: 155 RQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSLKATMIYVTHDQVEAM 214
           +QRV + R +  +P + L DE  S LD  +R   + E+ +L    K T+++++HD  EAM
Sbjct: 172 QQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISHDLDEAM 231

Query: 215 TLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFI-GSPQMNFIEAAKLGDGEAKTIGI 273
            + D+I ++  GR+ QVG+P E+   PA+ +V  F  G    N + A  +      TI I
Sbjct: 232 RIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRGVDPTNILTAGDIATQTQVTIPI 291


Lambda     K      H
   0.320    0.137    0.393 

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: 337
Number of extensions: 14
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: 352
Length of database: 415
Length adjustment: 30
Effective length of query: 322
Effective length of database: 385
Effective search space:   123970
Effective search space used:   123970
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 (21.8 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