GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Rhizobium freirei PRF 81

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_004116864.1 RHSP_RS11850 sugar ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>NCBI__GCF_000359745.1:WP_004116864.1
          Length = 402

 Score =  566 bits (1458), Expect = e-166
 Identities = 281/402 (69%), Positives = 336/402 (83%), Gaps = 4/402 (0%)

Query: 1   MSSANTTNEESNVISVGSYIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQ 60
           MSSAN   E S+V+S+G +IR+NIREYGMLIALV IM+ FQ+ T G+LFRP NLTN++LQ
Sbjct: 1   MSSANPATESSHVVSIGDHIRNNIREYGMLIALVVIMLLFQYLTNGVLFRPQNLTNIVLQ 60

Query: 61  NSFIVIMALGMLLVIVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGII 120
           NSFIVIMALGMLLVIVAGHIDLSVGS+V FVGA+A +L VQ  MN   A +ICL++G  +
Sbjct: 61  NSFIVIMALGMLLVIVAGHIDLSVGSVVGFVGAVAGVLVVQMHMNLAAATVICLLMGAAV 120

Query: 121 GAAQGYWIAYHRIPSFIVTLAGMLVFRGLTLFVLG----GKNIGPFPTDFQVISTGFLPD 176
           GA  GY+IAYHRIPSFIVTL+GMLVFRGLT  ++     G +IGPFP  FQV++TGF+PD
Sbjct: 121 GAWHGYFIAYHRIPSFIVTLSGMLVFRGLTYTIINTTGNGSSIGPFPPAFQVVATGFIPD 180

Query: 177 IGGIEGLNTTSMILTVLITVALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFL 236
              + G+ +TS+ LT+ I + +F L+WRRR VN KHGIDVEPF FF+ QNL+++ A +F+
Sbjct: 181 FVDMGGVRSTSIFLTIAIPIVMFLLSWRRRTVNEKHGIDVEPFSFFLGQNLVVAAATIFI 240

Query: 237 GYQLSTYRGLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFL 296
           GYQ+S+YRGLPNVLI+ML LIALYSF T+RTTIGRR+YAMGGNEKATKLSGI+T RL+F 
Sbjct: 241 GYQISSYRGLPNVLILMLALIALYSFATQRTTIGRRIYAMGGNEKATKLSGIDTRRLTFY 300

Query: 297 TFVNMGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGA 356
           TF+NMG+LA +AG+IIATRLNSAT K G G ELDVIAACFIGGASASGGVGK+TGAVIGA
Sbjct: 301 TFINMGILASIAGIIIATRLNSATAKGGDGLELDVIAACFIGGASASGGVGKVTGAVIGA 360

Query: 357 FIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAVFFDVYNKNKG 398
            IMGV+N GMSI+G   D Q+M+KG VLLAAVF DVYNKNKG
Sbjct: 361 LIMGVLNQGMSILGYQTDSQKMIKGAVLLAAVFIDVYNKNKG 402


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: 712
Number of extensions: 37
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: 398
Length of database: 402
Length adjustment: 31
Effective length of query: 367
Effective length of database: 371
Effective search space:   136157
Effective search space used:   136157
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.

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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