GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Desulfoscipio geothermicus DSM 3669

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_900115975.1:WP_092484009.1
          Length = 344

 Score =  188 bits (478), Expect = 2e-52
 Identities = 105/283 (37%), Positives = 166/283 (58%), Gaps = 22/283 (7%)

Query: 19  YSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMNDASPKDRD 78
           + + + NL++ + E+ + +GP+G GK+  L  IAG+    +G +   ++ +   +P+ R 
Sbjct: 14  FQLLDINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQRK 73

Query: 79  IAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEFLERKPADLSG 138
           +  V+Q+YAL+PH++V EN+ FG ++RK  K  I  ++ E   +LG+   L R P+ LSG
Sbjct: 74  VGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTLSG 133

Query: 139 GQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYVTHDQTE 198
           G++QR A+ RA++   ++ L+DEPLS LD + +   + E+ KIH+ +  TT++VTHD  E
Sbjct: 134 GEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDFNE 193

Query: 199 AMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIGSPAMNFFEVTV 258
           AM LAD+I +M            G+I Q+GTPQE++ +P N FVA F+G    N F    
Sbjct: 194 AMYLADKIGVMHQ----------GQIIQVGTPQEIFYKPQNDFVASFVG--IENIF---- 237

Query: 259 EKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDIS 301
             E  VN D +SLA       I    G  G KV + + PEDI+
Sbjct: 238 --EGQVNDDKVSLA---PDVDIFVNTGKQG-KVKVAVPPEDIA 274


Lambda     K      H
   0.318    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: 299
Number of extensions: 11
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: 344
Length adjustment: 29
Effective length of query: 348
Effective length of database: 315
Effective search space:   109620
Effective search space used:   109620
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 (21.7 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