GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Rhizorhabdus wittichii RW1

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  135 bits (341), Expect = 9e-37
 Identities = 80/202 (39%), Positives = 109/202 (53%), Gaps = 3/202 (1%)

Query: 25  NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTH--VAPRDRDIAMV 82
           +L I  G F+ LVG SG GK+T L+ +  L  +  G I I  +DV    VA   R I  V
Sbjct: 21  SLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIEGRDVAAQPVAELRRRIGYV 80

Query: 83  FQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGL-TEFLERKPKALSGGQR 141
           FQ   L+PHM+V EN+    ++ G  ++E   RV E    + L  +F ER+P  LSGGQ 
Sbjct: 81  FQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLDLVALPADFAERRPAQLSGGQA 140

Query: 142 QRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALT 201
           QRV   RA+   P + LMDEP   LD   R +      AL   +G+T++ VTHD  EAL 
Sbjct: 141 QRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALHEAMGLTSLIVTHDMAEALL 200

Query: 202 MGDRIAVLKDGYLQQVGAPREL 223
           + DR+ V+ +G +     PR L
Sbjct: 201 LADRVIVIGEGRILADQPPRAL 222


Lambda     K      H
   0.316    0.135    0.380 

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: 212
Number of extensions: 12
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 376
Length of database: 252
Length adjustment: 27
Effective length of query: 349
Effective length of database: 225
Effective search space:    78525
Effective search space used:    78525
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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