GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-transport in Pseudomonas fluorescens GW456-L13

Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate PfGW456L13_2481 Major facilitator family transporter

Query= reanno::WCS417:GFF1429
         (438 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2481
          Length = 441

 Score =  337 bits (864), Expect = 4e-97
 Identities = 171/411 (41%), Positives = 250/411 (60%), Gaps = 8/411 (1%)

Query: 21  LMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIMH 80
           ++PL +I +I++++DR NI   + H++ DLGI AAAYGLGAGLFF+ YAL E+PSN+++ 
Sbjct: 20  VLPLFVIMFIVNYIDRVNIGFVRSHMEHDLGIGAAAYGLGAGLFFIGYALFEVPSNILLQ 79

Query: 81  KVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNRE 140
           KVGAR W+ RIM+TWGL++A MAF+Q ET FY+LR LLG+AEAG FPGV+ Y T W    
Sbjct: 80  KVGARIWLTRIMLTWGLVAAGMAFIQNETHFYILRFLLGVAEAGFFPGVIYYFTRWLPGV 139

Query: 141 QRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVWRK 200
           +R +A   FL G   A++I GP+   L++++G LG HGWQWM+ +EG+ +V     VW  
Sbjct: 140 ERGKAIAIFLSGSALASLISGPLSGLLLQIEG-LGLHGWQWMYFIEGMFSVGLCVFVWFW 198

Query: 201 LPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWL-----TPQILLAIFVYFC 255
           L  RP  A WLS EE   + + I  + E+ A E    +K  L       QI+L   +YF 
Sbjct: 199 LDSRPHDAKWLSREEQDALVKAI--DDEQLAREAATPIKPSLGKLLKDRQIILFCLIYFF 256

Query: 256 HQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLV 315
            Q+TIY   F+LPSII K G+LS + VGL  S+PW+ + +G       +      +  + 
Sbjct: 257 IQLTIYAATFWLPSIIKKMGDLSDVQVGLFNSIPWLLSIVGMYAFASLSAKWKHQQAWVA 316

Query: 316 TGLLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVN 375
           T LL  A G+ +++  GPVF+ +  C +A+ F    S+ +  P + L     AG +  +N
Sbjct: 317 TALLIAAAGMFMSTTGGPVFAFVAICFAALGFKSASSLFWPIPQAYLDARIAAGVIALIN 376

Query: 376 ACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLRMGHEP 426
           + G LGGFV P+  G++E+ TG+   GL  +A   ++AA+     R   +P
Sbjct: 377 SVGNLGGFVAPTTFGLLEERTGSIQGGLYGLAATSIIAAIIVFAARNTPKP 427


Lambda     K      H
   0.327    0.141    0.438 

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: 580
Number of extensions: 38
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: 438
Length of database: 441
Length adjustment: 32
Effective length of query: 406
Effective length of database: 409
Effective search space:   166054
Effective search space used:   166054
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.

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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