GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Dshi_0546 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate Pf1N1B4_3974 ABC transporter, ATP-binding protein

Query= reanno::Dino:3607124
         (338 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3974 ABC transporter,
           ATP-binding protein
          Length = 341

 Score =  244 bits (624), Expect = 2e-69
 Identities = 131/324 (40%), Positives = 197/324 (60%), Gaps = 3/324 (0%)

Query: 1   MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60
           MA ++++ + K YG   A+   NL +E GEFV  +GPSGCGK+T L+ +AG   VSSGRI
Sbjct: 1   MAFVQLENLGKRYGEIDAVVATNLSVEKGEFVSLLGPSGCGKTTTLQMIAGFVEVSSGRI 60

Query: 61  EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120
            + GRD+T  +PA R L +VFQSYAL+PHMTVR+N+ FG+++     D  ++R+    ++
Sbjct: 61  VLDGRDITHAKPASRGLGVVFQSYALFPHMTVRDNVAFGLRMRKVPNDELQQRVDRVLKL 120

Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180
           ++L  + +R P +LSGGQRQRVA+ RA+V  P V L DEPLSNLDA LR +M+ E+  + 
Sbjct: 121 VRLNQHAERYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQ 180

Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240
           +++G T + VTHDQ EA++++D++VV+  GRI Q+ +P  LY  P + F++ F+G   + 
Sbjct: 181 REVGITTLMVTHDQSEALSISDRVVVMQAGRITQIDAPYTLYEHPRTEFISGFVGKANLL 240

Query: 241 VFSSDVG--LQDISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLLYLGLK 298
               D    +Q  + D     +  RPE I++   G G +   +  +  LG + L  +   
Sbjct: 241 PGERDSAGVVQVCNRDNGELTLSLRPEKIDLRDVGLGRLQGKIVSRFFLGSQWLYGVSTS 300

Query: 299 -GGGQIVARVGGDDETKVGAAVSL 321
            G   +V R  G      G AV L
Sbjct: 301 LGELSVVRRNDGSAPLIEGTAVGL 324


Lambda     K      H
   0.320    0.139    0.396 

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: 309
Number of extensions: 11
Number of successful extensions: 1
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: 338
Length of database: 341
Length adjustment: 28
Effective length of query: 310
Effective length of database: 313
Effective search space:    97030
Effective search space used:    97030
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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, 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