GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Mucilaginibacter mallensis MP1X4

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_091377242.1 BLU33_RS19840 ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_900105165.1:WP_091377242.1
          Length = 318

 Score =  143 bits (360), Expect = 7e-39
 Identities = 92/249 (36%), Positives = 143/249 (57%), Gaps = 7/249 (2%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I V+++SK F  GKV A+D+++  +   E   +LG SG GKTT +++I  L  P+ G+++
Sbjct: 2   IKVEHLSKHF--GKVKAVDDISFEVAEHETLVLLGTSGCGKTTTLKMINRLIEPTHGKIF 59

Query: 64  FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEE 123
            +++ +      ++    R IG V Q   L+P+ T  ENIA     +K   ++I+ RV E
Sbjct: 60  INNKNILDQQPEVLR---RGIGYVLQNNGLFPHYTVGENIAIVPQLLKWDVKKIQHRVSE 116

Query: 124 VAKILDIHH-VLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARAL 182
           + + L + +  LN +P ELSGGQQQRV LARALV +P +LL+DEPF  LD   +    A 
Sbjct: 117 LLEKLHLSNDYLNVYPNELSGGQQQRVGLARALVANPPVLLMDEPFGALDNVTKAKIHAE 176

Query: 183 VKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIG 242
            K +      T+++V+HD  + F + DR+ ++  GK+VQ G P +L   P +  V   + 
Sbjct: 177 FKALDELKRKTIIMVTHDVQEAFELGDRICLMDAGKIVQTGVPTELLFKPKNNFVRDFLN 236

Query: 243 EIN-ELEGK 250
           E   ELE K
Sbjct: 237 EQRLELEFK 245


Lambda     K      H
   0.319    0.139    0.390 

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: 274
Number of extensions: 16
Number of successful extensions: 3
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: 353
Length of database: 318
Length adjustment: 28
Effective length of query: 325
Effective length of database: 290
Effective search space:    94250
Effective search space used:    94250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 Sep 24 2021. 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