GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysP in Burkholderia phytofirmans PsJN

Align uncharacterized amino-acid permease C869.11 (characterized)
to candidate BPHYT_RS07280 BPHYT_RS07280 amino acid permease

Query= CharProtDB::CH_091412
         (580 letters)



>FitnessBrowser__BFirm:BPHYT_RS07280
          Length = 466

 Score =  180 bits (456), Expect = 1e-49
 Identities = 121/404 (29%), Positives = 194/404 (48%), Gaps = 23/404 (5%)

Query: 73  LKRSLKSRHMQMISIGGAIGTGLYVGSGSSLADGGPASVIINYSLIGIMMFFIVYALGEM 132
           L+R L +  + MI+IGGAIGTGL++GSG ++   GP SV+++Y++  ++   ++  L EM
Sbjct: 18  LQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGP-SVLVSYAIGALIALLLMGCLAEM 76

Query: 133 AVAYPVAGGFNTYATRFIDPAWGFAVSWNYFINYFVTFPLELTTCAITFRYW-TDINSAA 191
            VA+P +G F  YA  +I P  GF V + Y+ +       E+T  A+  +YW   +    
Sbjct: 77  TVAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTAIAVYMKYWFPAVPGWY 136

Query: 192 WISIFLVVIIIVNLFGVRAYGEVEFILSTVKVVATFGFIILAIIINCGGVPTDHRGYIGG 251
           WI  F   +I +N   V+ +G VE++ S +K+VA  GFI+L   +   G P D       
Sbjct: 137 WIVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLGAYV-VFGAPADSTIGFAN 195

Query: 252 SIIKHKPFRHGFKGFCSVFTTAAFSFSGTEVIGLAAAEVDNPQKALPHAVKQVFWRIAIF 311
                  F  G  G       + FS+   E+I +AA E  +PQKA+  A +   +R+  F
Sbjct: 196 YTSHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKAITRAFRATMFRLVFF 255

Query: 312 YVVSLILIGLLISPDDPNLMGNGSTSVSPFVLAIKEANIKGLPSVFNAVIIISVVSVTNS 371
           Y+++L L+ L I P          T  SPFV  +   ++ G   V N VI+++ +S  NS
Sbjct: 256 YLLTLALM-LAIVP-----WNAAGTDESPFVRVMAATHVPGAAGVINFVILVAALSAMNS 309

Query: 372 STYTAGRTLHGMANLKQAPSFFKYTDRLGRPLLAM-IVVLLFGFFAYINEADKNGNDVSD 430
             Y   R +  ++    AP      +  G P+ A+ +  +       +N          D
Sbjct: 310 QLYITTRMMFSLSRAGYAPRKLGALNGKGVPVAALWLSTIGIALATVLNVV------YPD 363

Query: 431 TVFNWLLALSGLSNFFTWGSICLCHIIFR-------LAFKKQGH 467
             F  ++++S     FTW  I + H  FR       LAF+  G+
Sbjct: 364 ASFVLMMSVSMFGAMFTWLMIFVTHFFFRHRHQGAPLAFRMWGY 407


Lambda     K      H
   0.325    0.141    0.429 

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: 688
Number of extensions: 44
Number of successful extensions: 5
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: 580
Length of database: 466
Length adjustment: 35
Effective length of query: 545
Effective length of database: 431
Effective search space:   234895
Effective search space used:   234895
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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:

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