GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SynE:Synpcc7942_1680
          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 (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