GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Methanospirillum lacunae Ki8-1

Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_109967995.1 DK846_RS05790 NAD-dependent epimerase/dehydratase family protein

Query= BRENDA::O73960
         (318 letters)



>NCBI__GCF_003173355.1:WP_109967995.1
          Length = 312

 Score =  284 bits (726), Expect = 2e-81
 Identities = 154/315 (48%), Positives = 206/315 (65%), Gaps = 8/315 (2%)

Query: 1   MRVLVTGGAGFIGSHLVDRLMEEGYKVRVLDDLSAGSLKNIEGWLGNENFEFIKGDMRDV 60
           MR +VTGGAGFIGSH+VD L+ +G +V V+D L AG L+ I   L +   +FI+ ++ + 
Sbjct: 1   MRSIVTGGAGFIGSHIVDHLVAQGDEVVVIDALLAGDLRFISRHLDSGAVKFIRANLLEP 60

Query: 61  EIVSKAVKDVDAVFHLAANPEVRIGSQSPELLYETNVLITYNLLNAVRNSGVKYLVFTSS 120
                     D V+H+AA+P+VR  + +P+      ++ T+ +L A+R   +  +VFTS+
Sbjct: 61  GW-QDVCAGADRVWHIAADPDVRESAVTPDAQLNNTIIATHRVLEAIRLHKIPEIVFTST 119

Query: 121 STVYGDAKVIPTPEDYAPLEPISVYGAAKLAAEALISGYAHTFDFRALIIRLANIIGKRS 180
           STVYG+A VIPTPE Y P+EP+SVYGAAKLA EALIS Y H+F  R  I R ANIIG RS
Sbjct: 120 STVYGEATVIPTPETYTPMEPVSVYGAAKLACEALISAYCHSFGVRGYIFRFANIIGPRS 179

Query: 181 NHGVIYDFINKLKANPNELEILGDGTQRKSYLHISDTIDGIMKLFEHFLNGEERVDFYNL 240
            HGVI DFI KL+ANP ELEILGDG Q KSYL ++  +  I  +  H     ++V+ YN+
Sbjct: 180 GHGVITDFIKKLRANPKELEILGDGKQTKSYLEVTACVAAISYVIAH---ANDQVNTYNI 236

Query: 241 GNEDWITVKEIAEIVSEEMNL-NPRFKFTGGVDGGRGWKGDVKLMLLSIEKAKRTGWKPR 299
           G+EDWI V  IA+I+ +E  L    +K+TG   G RGW GDV  M LS+EK K  G+ P 
Sbjct: 237 GSEDWIDVTTIADILVKEAGLAGVSYKYTG---GSRGWVGDVPKMQLSVEKLKSLGYTPT 293

Query: 300 MNSYEAVRKTVREML 314
           + S+E+VR  VR  L
Sbjct: 294 IGSHESVRLAVRAAL 308


Lambda     K      H
   0.318    0.138    0.397 

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: 283
Number of extensions: 15
Number of successful extensions: 4
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: 318
Length of database: 312
Length adjustment: 27
Effective length of query: 291
Effective length of database: 285
Effective search space:    82935
Effective search space used:    82935
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: 48 (23.1 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