GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Desulfacinum infernum DSM 9756

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_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::P96483
         (377 letters)



>NCBI__GCF_900129305.1:WP_073038605.1
          Length = 368

 Score =  298 bits (764), Expect = 1e-85
 Identities = 177/383 (46%), Positives = 232/383 (60%), Gaps = 24/383 (6%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           MA +  D+  + +       V    + + D EF+VLVGPSGCGKST+LRM+AGLE+V  G
Sbjct: 1   MAEIKLDQVNKRF--KKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSG 58

Query: 61  AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120
            I IG R V H+PPKDRDIAMVFQ+YALYPHM V  NM F L   GVP+ EI ++V++AA
Sbjct: 59  EISIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAA 118

Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180
           +IL ++  L R+P  LSGGQRQRVAMGRAIVR+PQ FL DEPLSNLDAKLRV  R ++A 
Sbjct: 119 EILGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAK 178

Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240
           L  RL  T VYVTHDQ+EAMT+ DR+ V+KDG + QV  P  +Y++PAN FVAGFIGSP+
Sbjct: 179 LHERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPS 238

Query: 241 MNLVEVPITD-------GGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGG 293
           MN ++V + +        G  F    VP +R A +     +R V  G+RPE  DV E  G
Sbjct: 239 MNFLDVRLVEEAGDLWVDGESF-RLKVPRHR-APAFRGHVNRPVIFGIRPE--DVKERPG 294

Query: 294 AVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGS 353
                      +    L   V+V E +G++  V  TA VG        R++         
Sbjct: 295 DAL-------PEGVEPLRAEVDVREPIGSE--VIITATVGSHA--FTARISPNVAVRVHD 343

Query: 354 TLHVVPRPGETHVFSTSTGERLS 376
            + +     + H+F   + + L+
Sbjct: 344 PIDLAVNMNKMHLFDPESEQALN 366


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: 416
Number of extensions: 16
Number of successful extensions: 1
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: 368
Length adjustment: 30
Effective length of query: 347
Effective length of database: 338
Effective search space:   117286
Effective search space used:   117286
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