GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Chryseobacterium viscerum 687B-08

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_103234822.1 C1634_RS14760 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_002899945.2:WP_103234822.1
          Length = 416

 Score =  146 bits (369), Expect = 8e-40
 Identities = 77/233 (33%), Positives = 133/233 (57%), Gaps = 1/233 (0%)

Query: 14  KKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYF-DDRLVASN 72
           K G  + ++  +  I  GE F I+G SG+GK+T +R +  L+ P++G++Y  DD + + N
Sbjct: 44  KTGCTIGINKASFEIYEGEFFVIMGLSGSGKSTLLRCLNRLNEPTSGKVYINDDDITSKN 103

Query: 73  GKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHH 132
            K ++     ++ MVFQ + L P+ T  +N  F L      K    ++ ++   I+ ++ 
Sbjct: 104 NKELLEVRRTEMSMVFQKFGLLPHHTILDNAGFGLEIRGEDKASRNEKAQKALDIVGLNG 163

Query: 133 VLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGV 192
             N +P +LSGG QQRV LARAL  DP +LL+DE FS LD  ++   +  + E+Q+ L  
Sbjct: 164 FENQYPSQLSGGMQQRVGLARALANDPEVLLMDEAFSALDPLIKSEMQDQMLELQNTLQK 223

Query: 193 TLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEIN 245
           T++ ++HD  +   I DR+ ++  G + Q+G  ED+  NP S  V + + +++
Sbjct: 224 TIVFITHDLDEAIKIGDRIVIMKDGVIEQIGTAEDILTNPASDYVKAFVEKVD 276


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: 322
Number of extensions: 14
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: 353
Length of database: 416
Length adjustment: 30
Effective length of query: 323
Effective length of database: 386
Effective search space:   124678
Effective search space used:   124678
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: 50 (23.9 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