GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Desulfoscipio geothermicus DSM 3669

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein

Query= uniprot:Q6MNM2
         (347 letters)



>NCBI__GCF_900115975.1:WP_092484009.1
          Length = 344

 Score =  199 bits (507), Expect = 7e-56
 Identities = 105/275 (38%), Positives = 164/275 (59%), Gaps = 14/275 (5%)

Query: 19  LKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGKKINDIEPQNRDIA 78
           L  I+L++  GE+ +++GP+G GK+ +L T+AG+   D GTI    + +  + P+ R + 
Sbjct: 16  LLDINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQRKVG 75

Query: 79  MVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQIKHLLDRKPKELSGGQ 138
            V+Q YAL+PH+TV EN+ FG +++ L    I  +++E+  +L I HLL+R P  LSGG+
Sbjct: 76  FVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTLSGGE 135

Query: 139 RQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKSTMIYVTHDQMEAT 198
           +QR AL RAL     ++L DEPLS LD   +   + E+K++H   K+T ++VTHD  EA 
Sbjct: 136 QQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDFNEAM 195

Query: 199 TLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFLEGAVLEKIPWPEARKA 258
            L D+I V+  G I Q+GTP EI+++P+N F+A+F+G    N  EG V            
Sbjct: 196 YLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVGIE--NIFEGQV-----------N 242

Query: 259 DQILGIRPDA-FALNQGPLGTQEVALGDFQIDISE 292
           D  + + PD    +N G  G  +VA+    I +S+
Sbjct: 243 DDKVSLAPDVDIFVNTGKQGKVKVAVPPEDIALSK 277


Lambda     K      H
   0.318    0.136    0.383 

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: 285
Number of extensions: 15
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: 347
Length of database: 344
Length adjustment: 29
Effective length of query: 318
Effective length of database: 315
Effective search space:   100170
Effective search space used:   100170
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.

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