GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Sinorhizobium fredii NGR234

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_164924745.1 NGR_RS30975 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::P96483
         (377 letters)



>NCBI__GCF_000018545.1:WP_164924745.1
          Length = 355

 Score =  333 bits (853), Expect = 6e-96
 Identities = 190/382 (49%), Positives = 248/382 (64%), Gaps = 34/382 (8%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           M  VT    T+ Y       + QL   IEDGEF+VLVGPSGCGKST LRMLAGLE+++GG
Sbjct: 1   MTDVTIRNVTKRYGALT--VIPQLSFRIEDGEFVVLVGPSGCGKSTLLRMLAGLEEISGG 58

Query: 61  AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120
            + +G   +   P K+RD+A+VFQNYALYPHMTVA+NMGFALK+   P+AEI ++V++AA
Sbjct: 59  DLLMGADVINDRPAKERDMAIVFQNYALYPHMTVAENMGFALKLRKRPRAEIDERVDKAA 118

Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180
            IL L + LDR P+ALSGGQRQRVAMGRAIVR+PQVFL DEPLSNLDAKLRV  R +I +
Sbjct: 119 AILGLGKLLDRYPRALSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKA 178

Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240
           L +RL ITTVYVTHDQ+EAMTM D++ V+ +G ++Q+ +P  +YD+PAN+FVAGFIGSP+
Sbjct: 179 LHQRLKITTVYVTHDQIEAMTMADKIVVMNEGRVEQMGTPLELYDRPANIFVAGFIGSPS 238

Query: 241 MNLVEVPITDGGVKFGNSVVPVNREALSAADKGDRT------VTVGVRPEHFDVVELGGA 294
           MN   +P T   V   N  +    E ++    G  T      VT G+RPEH  + E    
Sbjct: 239 MNF--LPAT---VAATNGPLLKTPEGVALPIDGGPTLTGRSEVTYGIRPEHLQLGE---- 289

Query: 295 VAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGST 354
                         G+   V VVE  G++  +Y T  VGG  +++V  +  R     G  
Sbjct: 290 -------------TGIPAEVVVVEPTGSETQLYVT--VGG--REVVAVLRDRVDVRPGEK 332

Query: 355 LHVVPRPGETHVFSTSTGERLS 376
           + + PR G  H+F  +TG R++
Sbjct: 333 IWLTPRKGCAHLFDPNTGARIA 354


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: 446
Number of extensions: 22
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: 377
Length of database: 355
Length adjustment: 30
Effective length of query: 347
Effective length of database: 325
Effective search space:   112775
Effective search space used:   112775
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: 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