GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Nocardiopsis lucentensis DSM 44048

Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate WP_017597434.1 D471_RS0103990 MFS transporter

Query= SwissProt::Q47421
         (501 letters)



>NCBI__GCF_000341125.1:WP_017597434.1
          Length = 433

 Score =  243 bits (619), Expect = 1e-68
 Identities = 144/418 (34%), Positives = 229/418 (54%), Gaps = 19/418 (4%)

Query: 23  RLRKAITAAALGNAMEWFDFGVYGFVA-YALGQVFFPG-ADPGVQMIAALATFSVPFLIR 80
           R  +A  AA +G  +EWFDF VY   A    G +FFPG  DP V ++A+ ATF+V F  R
Sbjct: 11  RPARAAVAAFVGTTIEWFDFYVYATAAGLVFGTLFFPGDIDPMVGLMASFATFAVGFFAR 70

Query: 81  PLGGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGF 140
           PLGGV FG  GD+ GR+  L  T+++M ++TFC+GL+P+Y ++G  AP+LL++ +  QG 
Sbjct: 71  PLGGVVFGHFGDRLGRKSALVTTLLMMGVATFCVGLLPTYAQVGFVAPLLLVVLRFVQGI 130

Query: 141 SVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWG 200
           +VGGE+ GA +   E +P+ ++ F GS+   G+ AG +L  G   LI T         WG
Sbjct: 131 AVGGEWGGAVLMAVESAPEERKTFYGSFAQLGNPAGALLATGSFGLI-TAWDSDLLYTWG 189

Query: 201 WRLPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGP-GVSFREIATHHW 259
           WRLPF  +  L L+GL +R  +EE+P F        +  R+   A P G   RE     W
Sbjct: 190 WRLPFLASCLLVLVGLVVRLKVEESPVF--------EAARENRAAEPEGPPLRETLRTSW 241

Query: 260 KSLLVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGM---LFVQPVM 316
           +++L+ IG++      YY++ T++ +Y       SE    LI+  + +     LF     
Sbjct: 242 RAVLLGIGVLPVAVGGYYVVTTFLQAYGVTEAGISEQ---LILSGLTLAAFVELFATLAT 298

Query: 317 GLLSDRFGRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMAST 376
             L DRFG    V +G  A+  LA+P F+++ +    LI L L ++ V + A  G +A  
Sbjct: 299 AWLGDRFGTARIVTVGLAAVAVLALPQFLVLETGSAVLIVLMLCLMRVAMAAVYGPIARV 358

Query: 377 LPALFPTHIRYSALASAFNIS-VLIAGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGL 433
           L  ++P  +RY+ ++ ++ ++  L  GL+P     L   + ++   A  L+V+A++ +
Sbjct: 359 LAQMYPPRVRYTGISVSYQVAGALFGGLSPLACTALFALTGSILSVAVLLVVMALVSI 416


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: 480
Number of extensions: 29
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: 433
Length adjustment: 33
Effective length of query: 468
Effective length of database: 400
Effective search space:   187200
Effective search space used:   187200
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 Apr 09 2024. 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