GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ac3H11_1693 in Synechococcus elongatus PCC 7942

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

Query= uniprot:A0A165KC86
         (260 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_1680 Synpcc7942_1680 Sulphate
           transport system permease protein 1
          Length = 338

 Score =  129 bits (325), Expect = 6e-35
 Identities = 75/241 (31%), Positives = 130/241 (53%), Gaps = 19/241 (7%)

Query: 8   VVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFE 67
           V ++V+ +SK+FG  QA+ DV +T++ G +  L+GP+G+GK+T   +I GL  PD+G   
Sbjct: 1   VGIQVSQVSKQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIF 60

Query: 68  LAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGF 127
           L G+     +V +     I   FQ+  LF  +T  +N+  G  +R               
Sbjct: 61  LTGRDATNESVRD---RQIGFVFQHYALFKHLTVRKNIAFGLELR--------------- 102

Query: 128 KAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAG 187
           K  +  +  R +ELL+ V +    D     LS G ++R+ +ARALA  PQ++ LDEP   
Sbjct: 103 KHTKEKVRARVEELLELVQLTGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGA 162

Query: 188 MNATEKVQLRELIDRIRND-NRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQK 246
           ++A  +  LR  + ++ ++ + T + + HD +  M + D++ V+++GK    G+PAE+  
Sbjct: 163 LDAKVRKDLRSWLRKLHDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYD 222

Query: 247 N 247
           N
Sbjct: 223 N 223


Lambda     K      H
   0.319    0.137    0.384 

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: 189
Number of extensions: 9
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: 260
Length of database: 338
Length adjustment: 26
Effective length of query: 234
Effective length of database: 312
Effective search space:    73008
Effective search space used:    73008
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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