GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artQ in Sinorhizobium meliloti 1021

Align Histidine transport system permease protein HisQ (characterized)
to candidate SMc02258 SMc02258 ABC transporter permease

Query= SwissProt::P52094
         (228 letters)



>lcl|FitnessBrowser__Smeli:SMc02258 SMc02258 ABC transporter
           permease
          Length = 241

 Score =  172 bits (436), Expect = 5e-48
 Identities = 91/214 (42%), Positives = 131/214 (61%)

Query: 4   GFSGVILQGALVTLELAISSVVLAVIIGLIGAGGKLSQNRLSGLIFEGYTTLIRGVPDLV 63
           G+ GV+LQG L ++E+A+    L + +G+ GA GKL    +   + E YTT++R VP+LV
Sbjct: 18  GWGGVLLQGFLSSIEIAVGGYALGLALGIGGAFGKLYGGPVLRDLLECYTTVVRAVPELV 77

Query: 64  LMLLIFYGLQIALNTVTEAMGVGQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPKGH 123
           L+LL++Y     LN +  A+GVG +DI  +VAGI  +G + GAY TE  RGA  AVP G 
Sbjct: 78  LILLLYYAGTDLLNQLLGAIGVGAVDISGLVAGIFVIGVVQGAYSTEVLRGAIKAVPAGQ 137

Query: 124 IEAATAFGFTRGQVFRRIMFPSMMRYALPGIGNNWQVILKSTALVSLLGLEDVVKATQLA 183
           IEAA A+G +   V RRI  P+M+ YA+PG+ N W +  K TAL++++G  ++   T+ A
Sbjct: 138 IEAARAYGMSPLLVLRRITLPAMLPYAIPGLANLWLIATKDTALLAVVGFSELTLVTRQA 197

Query: 184 GKSTWEPFYFAIVCGVIYLVFTTVSNGVLLFLER 217
             +T     F    G +YL  T VSN  +  LER
Sbjct: 198 AGATKAYLLFFCAAGALYLALTLVSNVFIGMLER 231


Lambda     K      H
   0.328    0.145    0.422 

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: 172
Number of extensions: 4
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: 228
Length of database: 241
Length adjustment: 23
Effective length of query: 205
Effective length of database: 218
Effective search space:    44690
Effective search space used:    44690
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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