GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proP in Paraburkholderia bryophila 376MFSha3.1

Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate H281DRAFT_00442 H281DRAFT_00442 MFS transporter, MHS family, proline/betaine transporter

Query= SwissProt::Q47421
         (501 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00442 H281DRAFT_00442 MFS
           transporter, MHS family, proline/betaine transporter
          Length = 489

 Score =  503 bits (1295), Expect = e-147
 Identities = 245/485 (50%), Positives = 347/485 (71%), Gaps = 10/485 (2%)

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

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

Query: 126 WAPILLLLAKMAQGFSVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVV 185
            AP LLL+A++ QGFS GGEY GA+ F+AE+S D++RGFMGS+L+FG++ G+VLGAG V 
Sbjct: 133 LAPALLLVARLVQGFSTGGEYGGAATFIAEFSTDKRRGFMGSFLEFGTLIGYVLGAGTVA 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  S R +    WK LL+C+GLV+  NVT YM L+Y+PSYLS +LH++E+HG+ I++ +
Sbjct: 249 VPKQSLRNLLMQQWKPLLLCVGLVLIFNVTDYMALSYLPSYLSATLHFNESHGLFIVLLV 308

Query: 306 MIGMLFVQPVMGLLSDRFGRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVI 365
           M+ M+ +    G LSD  GRKP ++ G V +F L++P+ +LI    +  +F GL++L V+
Sbjct: 309 MVLMMPMTLAAGRLSDTIGRKPVMLFGCVGLFALSIPALLLIRMGTLVPVFGGLMILGVL 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 LMGASLIGIVSVMALRETARKPLLGSGPCVATRAEAHAVLRG-----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: 666
Number of extensions: 24
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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