GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Croceitalea dokdonensis DOKDO 023

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_054557498.1 I595_RS00860 ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_001306415.1:WP_054557498.1
          Length = 219

 Score =  134 bits (337), Expect = 2e-36
 Identities = 79/224 (35%), Positives = 124/224 (55%), Gaps = 15/224 (6%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I   N+ K +  G +  L  V+I+I+ GE   I+GPSGAGKTT ++++  LD PS  +  
Sbjct: 2   ITATNIKKNY--GDLKVLKGVSISIKKGEVISIVGPSGAGKTTLLQLVGTLDTPSNPK-- 57

Query: 64  FDDRLVASNGKLIVPPEDRK--------IGMVFQTWALYPNLTAFENIAFPLTNMKMSKE 115
             D  +  NG  +    D++        IG +FQ   L P  TA EN+  P    K  K 
Sbjct: 58  --DSSIMINGVDVTDLRDKQLAKFRNENIGFIFQFHQLLPEFTALENVCIPAFIKKTPKA 115

Query: 116 EIRKRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARM 175
           +   R  E+   L +    +H PRELSGG+QQRVA+ARAL+ +PS++  DEP  NLD+  
Sbjct: 116 KAEVRGRELLDFLGLSQRYDHRPRELSGGEQQRVAVARALINNPSVIFADEPSGNLDSES 175

Query: 176 RDSARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKL 219
            ++   L  +++   G T ++V+H+  ++  +ADR  ++V G++
Sbjct: 176 AENLHQLFFKLREEFGQTFVIVTHN-KELANMADRKLIMVDGQI 218


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: 182
Number of extensions: 7
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: 219
Length adjustment: 25
Effective length of query: 328
Effective length of database: 194
Effective search space:    63632
Effective search space used:    63632
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: 47 (22.7 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