GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Brucella microti CCM 4915

Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate WP_004687208.1 BMI_RS13345 MHS family MFS transporter

Query= SwissProt::Q47421
         (501 letters)



>NCBI__GCF_000022745.1:WP_004687208.1
          Length = 426

 Score =  239 bits (610), Expect = 1e-67
 Identities = 134/424 (31%), Positives = 234/424 (55%), Gaps = 25/424 (5%)

Query: 24  LRKAITAAALGNAMEWFDFGVYGFVAYAL-GQVFFPGADPGVQMIAALATFSVPFLIRPL 82
           +R+ +TA+ +G  +E+FDF +Y   A  +   +FFP +D    ++ + ATF++ F  RP+
Sbjct: 14  VRRVLTASMIGTTIEFFDFYIYATAAVIVFPHLFFPASDGNSALLQSFATFAIAFFARPV 73

Query: 83  GGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSV 142
           G   FG  GDK GR+  L   ++ M +ST  IG +P+Y  IG+ AP+LL L ++ QG  +
Sbjct: 74  GAAIFGHFGDKIGRKATLVAALMTMGLSTVAIGFLPTYASIGVAAPLLLALCRLGQGLGL 133

Query: 143 GGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWR 202
           GGE+ GA +   E +P+ KR + G +   G+ AGF+L  G+ +L++  + E+ F A+GWR
Sbjct: 134 GGEWGGAVLLATENAPEGKRTWYGMFPQLGAPAGFILATGIFLLLAETMTEEQFFAYGWR 193

Query: 203 LPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSL 262
           +PF  +  L  +GL++R  + ETP F++ ++K E+           V   ++  HH  +L
Sbjct: 194 VPFIASAILVAVGLFIRLRIAETPEFQKAIDKAER---------VAVPAAQLFRHHKMNL 244

Query: 263 LVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGMLF---VQPVMGLL 319
            +     +AT V +Y++  +   + + +L YS       ++  MIG++F     P+  LL
Sbjct: 245 FLGTIGTMATFVLFYLMTVFSLGWGTRALGYSREE---FLVLQMIGVIFFGLTIPLSALL 301

Query: 320 SDRFGRKPFVVIGSVAM---FFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMAST 376
           SDR+G +  +VI +V +    F+  P F    + ++G + +G  ++ +       V+A  
Sbjct: 302 SDRYGMRTIMVIVTVLIGLYGFIMAPLFAAGTAGVLGFLIIGFGLMGMTYGPIGAVLAEP 361

Query: 377 LPALFPTHIRYSALASAFNIS-VLIAGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLT 435
               FPT +RY+  + AFN++ +L A L P +A WL       Y+  YY++  A+I L+ 
Sbjct: 362 ----FPTSVRYTGASLAFNLAGILGASLAPYIATWLATDYGFAYV-GYYMVAAAIISLIG 416

Query: 436 GLFM 439
            +F+
Sbjct: 417 FVFI 420


Lambda     K      H
   0.327    0.142    0.427 

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: 529
Number of extensions: 24
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: 501
Length of database: 426
Length adjustment: 33
Effective length of query: 468
Effective length of database: 393
Effective search space:   183924
Effective search space used:   183924
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 (21.7 bits)
S2: 51 (24.3 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