GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ppa in Azospirillum brasilense Sp245

Align Phenylacetate permease, Ppa (characterized)
to candidate AZOBR_RS19235 AZOBR_RS19235 actetate permease

Query= TCDB::O50471
         (520 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS19235 AZOBR_RS19235 actetate
           permease
          Length = 556

 Score =  691 bits (1782), Expect = 0.0
 Identities = 341/520 (65%), Positives = 417/520 (80%)

Query: 1   MNWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFL 60
           +N TAI+MF++FV  TL +T WA+ RTRSASDFYTAGGG++G QNGLAIAGD +SAA+FL
Sbjct: 37  VNVTAIAMFLLFVAGTLGITYWASKRTRSASDFYTAGGGISGFQNGLAIAGDYMSAAAFL 96

Query: 61  GISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTS 120
           G+S M+F  G+DG++Y +G L GWP++LFLIAERLRNLG++TFADV SYRL QTP+R  +
Sbjct: 97  GLSGMVFAKGFDGVIYTIGFLVGWPLMLFLIAERLRNLGRFTFADVASYRLGQTPIRSLA 156

Query: 121 AFGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQII 180
           A G+L V   YL+AQMVGAGKLI+LLFG+ Y YAV++VGVLM+ YVTFGGMLATTWVQII
Sbjct: 157 AVGSLTVVCFYLIAQMVGAGKLIQLLFGLDYTYAVVMVGVLMILYVTFGGMLATTWVQII 216

Query: 181 KAVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLG 240
           KAVMLL G + +  + L  FGF+ E +   AVA HA   AI+ P   +++P+ A+SL L 
Sbjct: 217 KAVMLLGGCTVLVGLALAQFGFNPERLLQQAVAAHAANAAILRPSAAMADPIAAVSLSLA 276

Query: 241 MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYR 300
           +M G AGLPHILMRFFTV DAKEARKSV YATGFIGYF++L + IGF AIV+VGT P+Y 
Sbjct: 277 LMCGPAGLPHILMRFFTVPDAKEARKSVVYATGFIGYFFILTVTIGFLAIVIVGTNPAYL 336

Query: 301 DATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYAC 360
           DA G I+GGGNM A+HL++A+GGNLFLGFISAVAFATILAVVAGL L+GASAVSHDLYA 
Sbjct: 337 DAAGKILGGGNMAAIHLSKAIGGNLFLGFISAVAFATILAVVAGLTLAGASAVSHDLYAR 396

Query: 361 VIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPVLLL 420
           V+++G ATE  EMRVSR+ATL +G++A+ LGL+FE+QNIAF+ GL   +AASVNFPVL+L
Sbjct: 397 VLKKGNATEASEMRVSRLATLALGVIAITLGLLFENQNIAFMVGLAFGLAASVNFPVLIL 456

Query: 421 SMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSLAFL 480
           S+FWKGLTTRGA  G  AGL S V  VVLGP VWV+V      +FPY +PALFSM +AF 
Sbjct: 457 SIFWKGLTTRGAFIGGFAGLVSCVAFVVLGPTVWVSVFKFPAPIFPYEHPALFSMVIAFA 516

Query: 481 SAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520
           + W+FSVTD S RA+ E   Y  Q+IRS TG+GAA A+ H
Sbjct: 517 TTWLFSVTDRSARAAAEAKAYEYQYIRSETGLGAASAASH 556


Lambda     K      H
   0.328    0.139    0.407 

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: 901
Number of extensions: 49
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: 520
Length of database: 556
Length adjustment: 35
Effective length of query: 485
Effective length of database: 521
Effective search space:   252685
Effective search space used:   252685
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 (21.8 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 paper from 2022 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