GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Burkholderia phytofirmans PsJN

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate BPHYT_RS30445 BPHYT_RS30445 ABC transporter substrate-binding protein

Query= SwissProt::P37735
         (333 letters)



>FitnessBrowser__BFirm:BPHYT_RS30445
          Length = 347

 Score =  132 bits (331), Expect = 2e-35
 Identities = 82/256 (32%), Positives = 142/256 (55%), Gaps = 10/256 (3%)

Query: 8   GALVGATALSLALSVPALAEPIVIKFSHVVA----PDTPKGKGAAKFEELAEKYTNGAVD 63
           GA + A     ++S  A+A P   +FS+ +A    P  P    A +      + TNG +D
Sbjct: 20  GATLSAAVPLWSVSRRAMAAP---EFSYKLATGQDPTHPVNIRAQEAINHIREATNGRLD 76

Query: 64  VEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHKV 123
           ++++P +QL  D + L  ++ G V+    + +    L      + +  + FKDY+A+ K 
Sbjct: 77  IKLFPQNQLGSDTDLLSQVRNGGVEFFNQASSILATL-TPAAGIVNTGFAFKDYDAVWKA 135

Query: 124 TQGEAGKMLLSKLEAKGITGLA-FWDNGFKIMSANT-PLTMPDDFLGLKMRIQSSKVLEA 181
             G+ G  +  ++   G+  ++  WDNGF+ +S++T  L  P D  G K+R+  + +L +
Sbjct: 136 MDGDLGNYIRGQIGKSGLVSVSKVWDNGFRQISSSTRALRAPADLKGFKIRVPQAPMLTS 195

Query: 182 EMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAV 241
              AL A P  + F+E+Y ALQTGVV+G ENP   + T K+ EVQK+ ++++H + GY +
Sbjct: 196 LFKALDAGPAPINFNELYSALQTGVVEGQENPLPIIATAKLYEVQKYISLTSHVWDGYWI 255

Query: 242 IVNKQFWDGLPADVRT 257
           + N+  W+ LPA++RT
Sbjct: 256 LGNRAAWERLPAEMRT 271


Lambda     K      H
   0.314    0.130    0.364 

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: 253
Number of extensions: 12
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: 333
Length of database: 347
Length adjustment: 28
Effective length of query: 305
Effective length of database: 319
Effective search space:    97295
Effective search space used:    97295
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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 (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