GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Phaeobacter inhibens BS107

Align TreV, component of Trehalose porter (characterized)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__Phaeo:GFF262
          Length = 348

 Score =  240 bits (612), Expect = 4e-68
 Identities = 134/301 (44%), Positives = 191/301 (63%), Gaps = 20/301 (6%)

Query: 3   VELIDIVKKYGKNI-VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIA 61
           V L  + K Y   +  +   + KIE GEF V++GPSG GKSTLL+++AG+E + +G +  
Sbjct: 4   VTLNSVRKVYPNGVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEGTLEI 63

Query: 62  DGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLG 121
               + +  P  R++AMVFQNYALYP+M+VR NIA+ LK R   + EI ++V +AAK+L 
Sbjct: 64  GDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAAKMLN 123

Query: 122 ISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKE 181
           + E LD+K +Q+SGGQ+QRVA+ RAIVR+P+ FL DEPLSNLDA++R   R E+K +Q+ 
Sbjct: 124 LEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKALQRR 183

Query: 182 LKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFL 241
           L  T IYVTHDQ EA+++ADRI +L+ G+ EQ+  P  +Y  P + +VA F+G  PMN L
Sbjct: 184 LGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPPMNLL 243

Query: 242 PGELMK------------------EKAQEIGFRPEWVE-VGKGNLSCMVESVEASGESRY 282
              +                    + A ++G RPE V+ V +G L+  VE +E  G  R 
Sbjct: 244 DATIANGQVTLPDGVSMGALDTSAQGAVKLGIRPEDVQLVAEGGLAIDVELIEELGAHRL 303

Query: 283 L 283
           L
Sbjct: 304 L 304


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: 262
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: 348
Length adjustment: 28
Effective length of query: 296
Effective length of database: 320
Effective search space:    94720
Effective search space used:    94720
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