GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Burkholderia phytofirmans PsJN

Align TreV, component of Trehalose porter (characterized)
to candidate BPHYT_RS35680 BPHYT_RS35680 sugar ABC transporter ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__BFirm:BPHYT_RS35680
          Length = 360

 Score =  234 bits (598), Expect = 2e-66
 Identities = 118/252 (46%), Positives = 172/252 (68%), Gaps = 1/252 (0%)

Query: 3   VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62
           V+L  I K+YG   V++GI   I+ GEF V++GPSG GKSTL++++AG+E++  G ++  
Sbjct: 4   VQLSGIFKRYGDTQVVHGIDLDIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDLMIG 63

Query: 63  GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122
           G       P++RN++MVFQ+YALYP++SV +NIAF  ++R         R+E AAK+L +
Sbjct: 64  GTRANSLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESSASFKPRIEAAAKMLNL 123

Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182
              LD+    +SGGQ+QRVA+ RA+VR PS FL DEPLSNLDA++R   R E+K + + L
Sbjct: 124 GGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALHQRL 183

Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242
           K T IYVTHDQ EA+++ADRI +++ G+ EQ+  P  LY++P   +VA F+G   MNF  
Sbjct: 184 KNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSMNFAE 243

Query: 243 GELMKEKAQEIG 254
           G ++  +AQ  G
Sbjct: 244 G-VIASRAQGQG 254


Lambda     K      H
   0.318    0.137    0.385 

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: 276
Number of extensions: 6
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: 324
Length of database: 360
Length adjustment: 29
Effective length of query: 295
Effective length of database: 331
Effective search space:    97645
Effective search space used:    97645
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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