GapMind for catabolism of small carbon sources

 

Alignments for a candidate for satP in Desulfovibrio vulgaris Miyazaki F

Align Succinate-acetate/proton symporter SatP; Succinate-acetate transporter protein (characterized)
to candidate 8501343 DvMF_2076 GPR1/FUN34/yaaH family protein (RefSeq)

Query= SwissProt::P0AC98
         (188 letters)



>FitnessBrowser__Miya:8501343
          Length = 183

 Score =  259 bits (661), Expect = 3e-74
 Identities = 122/180 (67%), Positives = 146/180 (81%)

Query: 4   TKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQIFAGLLEYKKGNT 63
           TKLANPAPLGLMGFGMTTILLN+HN G+F +  +ILAMGIFYGGIAQ+ AG++E+KKGNT
Sbjct: 3   TKLANPAPLGLMGFGMTTILLNIHNAGFFPISSMILAMGIFYGGIAQVIAGIMEFKKGNT 62

Query: 64  FGLTAFTSYGSFWLTLVAILLMPKLGLTDAPNAQFLGVYLGLWGVFTLFMFFGTLKGARV 123
           FG TAFTSYG FWLTLVA+++MPKLG  +     ++G YL +WG+FT FMF GTLKG   
Sbjct: 63  FGTTAFTSYGLFWLTLVALIVMPKLGWAEPTPHAYMGFYLAMWGLFTFFMFLGTLKGKTT 122

Query: 124 LQFVFFSLTVLFALLAIGNIAGNAAIIHFAGWIGLICGASAIYLAMGEVLNEQFGRTVLP 183
           L+F+F SLTVLFALLAI +  G+  I   AGW G++CGASA YLAM EVL+EQ+GR VLP
Sbjct: 123 LKFIFLSLTVLFALLAIRDFTGSELIGTIAGWEGIVCGASACYLAMAEVLHEQYGRVVLP 182


Lambda     K      H
   0.330    0.147    0.457 

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: 223
Number of extensions: 5
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: 188
Length of database: 183
Length adjustment: 19
Effective length of query: 169
Effective length of database: 164
Effective search space:    27716
Effective search space used:    27716
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 44 (21.6 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