GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Malonomonas rubra DSM 5091

Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= TCDB::P96483
         (377 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  146 bits (368), Expect = 1e-39
 Identities = 86/249 (34%), Positives = 131/249 (52%), Gaps = 18/249 (7%)

Query: 21  VDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPP------ 74
           V      I  GE  V++G SG GKST +RML  L +   G + I   D+  +        
Sbjct: 46  VQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKV 105

Query: 75  KDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPK 134
           +   ++MVFQ++AL PHMTV  N  F L++ GV K    Q+  +A + + L  + +  P 
Sbjct: 106 RRAKLSMVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPD 165

Query: 135 ALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTH 194
            LSGG +QRV + R +  +P + LMDE  S LD  +R   + ++  LQ +   T V+++H
Sbjct: 166 ELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISH 225

Query: 195 DQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFI-GSPAMNL---------- 243
           D  EAM +GDR+A+++ G + QV +P  +   PA+ +V  F  G    N+          
Sbjct: 226 DLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRGVDPTNILTAGDIATQT 285

Query: 244 -VEVPITDG 251
            V +PITDG
Sbjct: 286 QVTIPITDG 294


Lambda     K      H
   0.317    0.135    0.379 

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: 354
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: 377
Length of database: 415
Length adjustment: 31
Effective length of query: 346
Effective length of database: 384
Effective search space:   132864
Effective search space used:   132864
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