GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proP in Burkholderia phytofirmans PsJN

Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate BPHYT_RS12995 BPHYT_RS12995 MFS transporter

Query= SwissProt::Q47421
         (501 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS12995 BPHYT_RS12995 MFS
           transporter
          Length = 489

 Score =  504 bits (1297), Expect = e-147
 Identities = 244/485 (50%), Positives = 347/485 (71%), Gaps = 10/485 (2%)

Query: 6   KRVKPIALDDVTIIDDGRLRKAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQ 65
           K  + ++LDD+T++D   L++A+ A ALGNAMEWFDFGVY ++A  LG+VFFP A P  Q
Sbjct: 13  KEEQRLSLDDITVVDKSLLKRAVGAMALGNAMEWFDFGVYSYIAVTLGKVFFPSASPAAQ 72

Query: 66  MIAALATFSVPFLIRPLGGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGI 125
           +IA   TF+  FL+RP+GG+ FG LGD+ GRQ++LA+T+I+M++ TF IGLIPSY  IGI
Sbjct: 73  LIATFGTFAAAFLVRPVGGMVFGPLGDRIGRQRVLAMTMIMMALGTFAIGLIPSYTTIGI 132

Query: 126 WAPILLLLAKMAQGFSVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVV 185
           +AP+LLL+A++ QGFS GGEY GA+ F+AE+S D++RGFMGS+L+FG++ G+VLGAG V 
Sbjct: 133 FAPMLLLVARLVQGFSTGGEYGGAATFIAEFSTDKRRGFMGSFLEFGTLIGYVLGAGTVA 192

Query: 186 LISTLIGEQAFLAWGWRLPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKA 245
           +++  +   A L+WGWR+PF +A PLGL+GLY+R  LEETPAF++  E+ E  D    KA
Sbjct: 193 VLTATLSNDALLSWGWRVPFLIAGPLGLVGLYIRMKLEETPAFKKQAEQREAED----KA 248

Query: 246 GPGVSFREIATHHWKSLLVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAI 305
            P  SF ++    WK LL+C+GLV+  NVT YM L+Y+PSYLS +LH++E HG+ +++ +
Sbjct: 249 VPKQSFGQLLAQQWKPLLLCVGLVLIFNVTDYMALSYLPSYLSATLHFNETHGLFLVLLV 308

Query: 306 MIGMLFVQPVMGLLSDRFGRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVI 365
           M+ M+ +    G LSD  GRKP ++ G V +F L++P+ +LI    +  +F GL++L V+
Sbjct: 309 MVLMMPMTLAAGRLSDTIGRKPVMLFGCVGLFALSIPALLLIRMGTVLPVFGGLMILGVL 368

Query: 366 LNAFTGVMASTLPALFPTHIRYSALASAFNISV-LIAGLTPTVAAWLVESSQNLYMPAYY 424
           L+ FTGVM S LPALFPT IRY ALA  FNISV L  G TP V AWLV+ + NL MPAYY
Sbjct: 369 LSCFTGVMPSALPALFPTKIRYGALAIGFNISVSLFGGTTPLVTAWLVDRTGNLMMPAYY 428

Query: 425 LMVIAVIGLLTGLFMKETANKPLKGATPAASDLSEAKEILQEHHDNIEHKIEDITQQIAE 484
           LM  ++IG+++ + ++ETA KPL G+ P  +  +EA  +L+      E + E++ ++ A 
Sbjct: 429 LMGASLIGIVSVVALRETARKPLLGSGPCVATRAEAHAVLRG-----EREAEEMDERYAA 483

Query: 485 LEAKR 489
               R
Sbjct: 484 TATAR 488


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: 684
Number of extensions: 27
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: 501
Length of database: 489
Length adjustment: 34
Effective length of query: 467
Effective length of database: 455
Effective search space:   212485
Effective search space used:   212485
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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