GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Sinorhizobium fredii NGR234

Align TreV, component of Trehalose porter (characterized)
to candidate WP_164924745.1 NGR_RS30975 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q97ZC0
         (324 letters)



>NCBI__GCF_000018545.1:WP_164924745.1
          Length = 355

 Score =  250 bits (638), Expect = 4e-71
 Identities = 134/324 (41%), Positives = 202/324 (62%), Gaps = 24/324 (7%)

Query: 3   VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62
           V + ++ K+YG   VI  ++ +IE GEF V++GPSG GKSTLL++LAG+E++  G ++  
Sbjct: 4   VTIRNVTKRYGALTVIPQLSFRIEDGEFVVLVGPSGCGKSTLLRMLAGLEEISGGDLLMG 63

Query: 63  GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122
              I D+P ++R++A+VFQNYALYP+M+V +N+ F LK+R   + EI ERV+KAA +LG+
Sbjct: 64  ADVINDRPAKERDMAIVFQNYALYPHMTVAENMGFALKLRKRPRAEIDERVDKAAAILGL 123

Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182
            ++LD+    +SGGQ+QRVA+ RAIVR+P  FL DEPLSNLDA++R   R E+K + + L
Sbjct: 124 GKLLDRYPRALSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKALHQRL 183

Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242
           K T +YVTHDQ EA+++AD+I ++++G+ EQ+  P  LY+ P   +VA F+G   MNFLP
Sbjct: 184 KITTVYVTHDQIEAMTMADKIVVMNEGRVEQMGTPLELYDRPANIFVAGFIGSPSMNFLP 243

Query: 243 -------GELMK-----------------EKAQEIGFRPEWVEVGKGNLSCMVESVEASG 278
                  G L+K                       G RPE +++G+  +   V  VE +G
Sbjct: 244 ATVAATNGPLLKTPEGVALPIDGGPTLTGRSEVTYGIRPEHLQLGETGIPAEVVVVEPTG 303

Query: 279 ESRYLICNFKNNNITILSQEFYDV 302
               L        +  + ++  DV
Sbjct: 304 SETQLYVTVGGREVVAVLRDRVDV 327


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: 307
Number of extensions: 11
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: 355
Length adjustment: 28
Effective length of query: 296
Effective length of database: 327
Effective search space:    96792
Effective search space used:    96792
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 Apr 09 2024. 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