GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Pseudomonas simiae WCS417

Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate GFF1418 PS417_07205 LysR family transcriptional regulator

Query= SwissProt::Q47421
         (501 letters)



>FitnessBrowser__WCS417:GFF1418
          Length = 439

 Score =  248 bits (632), Expect = 4e-70
 Identities = 140/413 (33%), Positives = 222/413 (53%), Gaps = 7/413 (1%)

Query: 25  RKAITAAALGNAMEWFDFGVYGFVA-YALGQVFFPGADPGVQMIAALATFSVPFLIRPLG 83
           R+A  AA +G  +EW+DF +Y   A    GQ+FFP  D     +AA  TF+V F  RPLG
Sbjct: 10  RRAAAAAFIGTMIEWYDFYIYATAAALVFGQLFFPSDDKLFSTMAAFGTFAVGFFARPLG 69

Query: 84  GVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVG 143
           G+ FG +GD+ GR+K L IT+++M + T CIGL+P+Y +IG  AP+LL+L ++ QG +VG
Sbjct: 70  GIVFGHIGDRIGRKKSLVITLVMMGVVTVCIGLLPTYAQIGAAAPVLLVLLRVVQGIAVG 129

Query: 144 GEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRL 203
           GE+ GA +   E++P  +R F  S+   GS AG +L   +     T + E   L+WGWR+
Sbjct: 130 GEWGGAVLMAGEHAPKGRRNFFASFAQLGSPAGLILSL-LAFSAVTRLPEDELLSWGWRV 188

Query: 204 PFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSLL 263
           PF  +  L ++GL +R  + E+P F +     E+         P +   E+    W+ LL
Sbjct: 189 PFLASALLLVVGLAIRLGVNESPEFLEDKALAEKARAIKKDQAPVI---EVLRTAWRPLL 245

Query: 264 VCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGMLFVQPVMGLLSDRF 323
           +CIG         Y   T+M +Y +  L    +  +  +  + I    VQP+   ++++ 
Sbjct: 246 LCIGANTLGIAGVYFTNTFMIAYSTQQLGLPRSLILECLFFVAIIQFCVQPLAAWVAEKV 305

Query: 324 GRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMASTLPALFPT 383
           G   F+   +V       P F+L++S    LI LG+ +  V + +F  V+A  +  LF T
Sbjct: 306 GATRFLCAMTVLAMASPYPMFVLVSSGQAPLIILGIALAVVCMASFYAVIAGFVSGLFET 365

Query: 384 HIRYSALASAFNI-SVLIAGLTPTVAAWLVESSQNLYMP-AYYLMVIAVIGLL 434
            +RY+A++ A+ +   L  GLTP +  WL    Q  + P A +  +IA + L+
Sbjct: 366 RVRYTAISLAYQVCGALAGGLTPLIGTWLAHEYQGQWWPMAVFYSLIAAVSLV 418


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: 483
Number of extensions: 29
Number of successful extensions: 6
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: 439
Length adjustment: 33
Effective length of query: 468
Effective length of database: 406
Effective search space:   190008
Effective search space used:   190008
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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