GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_00442
          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:

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