GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Halococcus hamelinensis 100A6

Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_007694028.1 C447_RS11475 NAD-dependent epimerase/dehydratase family protein

Query= BRENDA::A3MUJ4
         (312 letters)



>NCBI__GCF_000336675.1:WP_007694028.1
          Length = 197

 Score =  118 bits (296), Expect = 1e-31
 Identities = 74/175 (42%), Positives = 100/175 (57%), Gaps = 4/175 (2%)

Query: 3   IVVTGGAGFIGSHLVDKLVELGYEVVVVDNLSSGRREFVNPSAELHVRDLKDYSW-GAGI 61
           +VVTGG+GFIGSHLV+ +     +V VVD     +        ++   D++D +   A +
Sbjct: 10  VVVTGGSGFIGSHLVEAVAPTN-DVRVVDTAGGQQSRRFPTDVDVVTGDVRDAATRDAAL 68

Query: 62  KG-DVVFHFAANPEVRLSTTEPIVHFNENVVATFNVLEWARQTGVRTVVFASSSTVYGDA 120
            G DV+FH AA   V  S  EP      NV AT ++LE AR+TG R VVFASS+ +YGD 
Sbjct: 69  DGADVLFHEAAIASVERSIEEPEESHAVNVDATLSLLETARRTGTR-VVFASSAAIYGDP 127

Query: 121 DVIPTPEEEPYKPISVYGAAKAAGEVMCATYARLFGVRCLAVRYANVVGPRLRHG 175
           D +P  E+EP  P S YG  K +G+  C  Y  L+ V  +++RY NV GPR   G
Sbjct: 128 DRVPVSEDEPKAPNSPYGLEKLSGDHYCRLYNHLYDVETVSLRYFNVYGPRQSAG 182


Lambda     K      H
   0.320    0.137    0.409 

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: 177
Number of extensions: 9
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: 312
Length of database: 197
Length adjustment: 24
Effective length of query: 288
Effective length of database: 173
Effective search space:    49824
Effective search space used:    49824
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 (21.8 bits)
S2: 46 (22.3 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