GapMind for catabolism of small carbon sources

 

Alignments for a candidate for permease in Burkholderia phytofirmans PsJN

Align Aromatic amino acid permease, AroP (characterized)
to candidate BPHYT_RS21680 BPHYT_RS21680 amino acid permease-associated protein

Query= TCDB::Q46065
         (463 letters)



>FitnessBrowser__BFirm:BPHYT_RS21680
          Length = 476

 Score =  325 bits (832), Expect = 3e-93
 Identities = 181/465 (38%), Positives = 268/465 (57%), Gaps = 15/465 (3%)

Query: 8   LGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMA 67
           L  GL+ RH+TM+ LG  IGAGLF+G+GV ++ AGPA +L+++I GA+VVLVM+MLGEMA
Sbjct: 10  LKAGLKQRHMTMIALGGVIGAGLFVGSGVVVQQAGPAAVLSFLITGALVVLVMRMLGEMA 69

Query: 68  AARPASGSFSRY------GEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWF-G 120
            A PA GSF  Y      G+ A G+ AGF  GW+YW+  ++V+  E    A ++  W   
Sbjct: 70  CAMPAVGSFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGAKLVQFWLPD 129

Query: 121 VEPWIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTF 180
           V  W  SLV +V     NLV+V  +GEFE+WFA IKVA I+ FL +G   + G  P +  
Sbjct: 130 VPAWAISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLGGMYVLGLWPAAKH 189

Query: 181 VGT--SNFIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAV 238
           V       +   G MP GI  V +G +A    + G EIVTIAAAE+ +P +A++ A  +V
Sbjct: 190 VTAVLPTLLSHGGLMPKGIGPVLSGAVAATGFYFGAEIVTIAAAEAQEPAKAVAKATNSV 249

Query: 239 IWRISVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALL 298
           I R+ VFY+GS+L++  L+P+ S   A     +P+   L    IP     M AI++ A+L
Sbjct: 250 ITRVLVFYVGSILLVVALVPWNSPKMA-----TPYVSALDAMGIPAAASVMNAIVLTAVL 304

Query: 299 SAFNAQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAG 358
           SA N+ +YA SR++F++    DAP   +K++   VP  A+L+   F + SV + Y +P  
Sbjct: 305 SALNSGLYAASRMIFALTRHGDAPAALAKVNRRGVPVRAILIGTVFGYASVVMSYVSPDT 364

Query: 359 LLDFLLNAVGGCLIVVWAMITLSQLKLRKELQAN-DEISTVRMWAHPWLGILTLVLLAGL 417
           +  FL+N+ G   I V+ +I +SQLKLR  ++ +  E   VRMW +P+L  + ++ + G+
Sbjct: 365 VFAFLVNSYGTVAIFVYVLIAISQLKLRARIERDAPEKLRVRMWCYPYLTWVAIIGMVGI 424

Query: 418 VALMLGDAASRSQVYSVAIVYGFLVLLSFVTVNSPLRGGRTPSDL 462
           +  M      R  ++      G L+L   + V  P  G   P  L
Sbjct: 425 LVAMAFIPEQRQPLWFGVASLGVLLLAYLLRVRKPDAGFGEPDTL 469


Lambda     K      H
   0.327    0.140    0.428 

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: 589
Number of extensions: 33
Number of successful extensions: 7
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: 463
Length of database: 476
Length adjustment: 33
Effective length of query: 430
Effective length of database: 443
Effective search space:   190490
Effective search space used:   190490
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