GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Desulfoscipio geothermicus DSM 3669

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_900115975.1:WP_092484009.1
          Length = 344

 Score =  184 bits (468), Expect = 2e-51
 Identities = 92/268 (34%), Positives = 157/268 (58%), Gaps = 9/268 (3%)

Query: 25  NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84
           NLE+ +GE+ +++GP+G GK+  L  +AG+     G I   ++++  +AP  R +  V+Q
Sbjct: 20  NLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQRKVGFVYQ 79

Query: 85  NYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQRQRV 144
           +YAL+PH+TV EN+ F  +I    +  I  ++DE  A LG+   L R P  LSGG++QR 
Sbjct: 80  DYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTLSGGEQQRT 139

Query: 145 AMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALTMGD 204
           A+ RA++ +P++ L+DEPLS LD + +   + ++  + + L  TT++VTHD  EA+ + D
Sbjct: 140 ALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDFNEAMYLAD 199

Query: 205 RIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARIKLSP 264
           +I V+  G + QVG P+E++ +P N FVA F+G    N+    V D        ++ L+P
Sbjct: 200 KIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVG--IENIFEGQVNDD-------KVSLAP 250

Query: 265 ETLAAMTPEDNGRITIGFRPEALEIIPE 292
           +    +     G++ +   PE + +  E
Sbjct: 251 DVDIFVNTGKQGKVKVAVPPEDIALSKE 278


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: 305
Number of extensions: 17
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: 376
Length of database: 344
Length adjustment: 29
Effective length of query: 347
Effective length of database: 315
Effective search space:   109305
Effective search space used:   109305
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