GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Synechococcus elongatus PCC 7942

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1

Query= uniprot:A0A165KQ08
         (355 letters)



>FitnessBrowser__SynE:Synpcc7942_1680
          Length = 338

 Score =  221 bits (564), Expect = 2e-62
 Identities = 112/236 (47%), Positives = 162/236 (68%), Gaps = 4/236 (1%)

Query: 5   LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64
           + ++ ++K+FG    S + ++ VD+ V  G  + L+GPSG GKSTLL +IAGL++P  G 
Sbjct: 3   IQVSQVSKQFG----SFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGR 58

Query: 65  IRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAA 124
           I + G++      RDR I  VFQ YAL+  L+V  NI F LE+RK  K + + R++E+  
Sbjct: 59  IFLTGRDATNESVRDRQIGFVFQHYALFKHLTVRKNIAFGLELRKHTKEKVRARVEELLE 118

Query: 125 MLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRL 184
           ++Q++ L DR PSQLSGGQRQRVA+ RALA QPQ+ L DEP   LDAK+R ++R+ +++L
Sbjct: 119 LVQLTGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSWLRKL 178

Query: 185 HQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG 240
           H    +T+V+VTHDQ EAM +  +I VM  G V+Q+G+P EIY+ PA  +V +FIG
Sbjct: 179 HDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFIG 234


Lambda     K      H
   0.318    0.135    0.388 

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: 326
Number of extensions: 10
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: 355
Length of database: 338
Length adjustment: 29
Effective length of query: 326
Effective length of database: 309
Effective search space:   100734
Effective search space used:   100734
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.

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:

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