GapMind for catabolism of small carbon sources

 

Alignments for a candidate for satP in Methanospirillum stamsii Pt1

Align Succinate-acetate/proton symporter SatP; Succinate-acetate transporter protein (characterized)
to candidate WP_109942323.1 DLD82_RS16975 hypothetical protein

Query= SwissProt::P0AC98
         (188 letters)



>NCBI__GCF_003173335.1:WP_109942323.1
          Length = 198

 Score =  211 bits (536), Expect = 9e-60
 Identities = 105/179 (58%), Positives = 127/179 (70%), Gaps = 1/179 (0%)

Query: 7   ANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQIFAGLLEYKKGNTFGL 66
           ANPAPLGL+GFGMTT+LLNLHN G F L  +ILAMG+ YGG AQI AGL+E+KK NTFG 
Sbjct: 17  ANPAPLGLLGFGMTTVLLNLHNAGLFTLGSMILAMGLCYGGTAQIIAGLMEWKKNNTFGT 76

Query: 67  TAFTSYGSFWLTLVAILLMPKLGLTDAPNAQF-LGVYLGLWGVFTLFMFFGTLKGARVLQ 125
           TAF SYG FW++LV IL+ P  GLT+       +  YL +WG+FT  MF GTL   R +Q
Sbjct: 77  TAFLSYGLFWISLVLILIFPVAGLTEGTGGNIAMASYLIMWGIFTSIMFLGTLMFNRAMQ 136

Query: 126 FVFFSLTVLFALLAIGNIAGNAAIIHFAGWIGLICGASAIYLAMGEVLNEQFGRTVLPI 184
           FVF SL +LF LLAIG+I G   I   AG  G+ICG SAIY  + +VLNE +G+ V P+
Sbjct: 137 FVFASLAILFFLLAIGDITGIQEITRIAGIEGIICGFSAIYTGLAQVLNEAYGKVVWPV 195


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: 183
Number of extensions: 11
Number of successful extensions: 3
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: 198
Length adjustment: 20
Effective length of query: 168
Effective length of database: 178
Effective search space:    29904
Effective search space used:    29904
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 24 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