GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Oscillibacter ruminantium GH1

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_040659170.1 ON16_RS02715 sugar ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>NCBI__GCF_000307265.1:WP_040659170.1
          Length = 404

 Score =  325 bits (833), Expect = 1e-93
 Identities = 174/387 (44%), Positives = 251/387 (64%), Gaps = 16/387 (4%)

Query: 24  IREYGMLIALVAIMVFFQFYTGGILFRPV--------NLTNLILQNSFIVIMALGMLL-V 74
           +++  M+IALV + + F+     +  +PV        N++NLI QNS++VI+A+GML+ +
Sbjct: 17  LKKNTMVIALVLVTLLFEVLIITVAHKPVSQALLTPANISNLISQNSYVVILAVGMLMCI 76

Query: 75  IVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIP 134
           +  G+IDLSVGS+VA VGA+A  L V   MN +LA +ICL++G  IGA Q YWIAY RIP
Sbjct: 77  LTGGNIDLSVGSVVALVGAVAGTLIVNMHMNIYLAMVICLLVGLAIGAWQAYWIAYVRIP 136

Query: 135 SFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLI 194
            FIVTLAGML++RGL   +L G  I  +P  +  +   ++P   G     +T + +T++I
Sbjct: 137 PFIVTLAGMLLWRGLAQIILDGLTISGYPETYLNLFNSYIP---GASAEKSTILTVTLVI 193

Query: 195 TVAL--FYLAWR--RRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVL 250
            V L   YLA +   R    ++  + +    F  +N ++   +L L   L  ++GLP +L
Sbjct: 194 GVVLCAVYLAVQLMNRAKRKRNHYETQSASMFWGKNAVLCALMLALCLMLGNHKGLPTIL 253

Query: 251 IVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGM 310
           I++ V++ +Y + T+ T  GR +YAMGGNEKA KLSGINT R  F  + NM  L+ +A +
Sbjct: 254 ILLAVIVLIYGYYTQNTVPGRHLYAMGGNEKAAKLSGINTNRTMFFAYTNMAFLSAVAAL 313

Query: 311 IIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVG 370
           ++  R NSA P AG  +E+D I ACFIGGASA GG G + GAV+GA  MGV+NNGMSI+G
Sbjct: 314 VVTARFNSAAPSAGTSYEMDAIGACFIGGASAYGGTGTVAGAVVGAVFMGVINNGMSILG 373

Query: 371 LGIDFQQMVKGLVLLAAVFFDVYNKNK 397
           +  ++Q++VKGLVLLAAV FDV +K +
Sbjct: 374 IDANWQKVVKGLVLLAAVIFDVVSKRR 400


Lambda     K      H
   0.329    0.145    0.422 

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: 547
Number of extensions: 32
Number of successful extensions: 5
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: 398
Length of database: 404
Length adjustment: 31
Effective length of query: 367
Effective length of database: 373
Effective search space:   136891
Effective search space used:   136891
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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