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_2493 Synpcc7942_2493 ATPase

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__SynE:Synpcc7942_2493
          Length = 253

 Score =  225 bits (574), Expect = 6e-64
 Identities = 118/249 (47%), Positives = 167/249 (67%), Gaps = 1/249 (0%)

Query: 9   VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68
           +L++  +++RFGGL A++ V   ++ G+++GLIGPNGAGKTT FN+ITGL     G    
Sbjct: 3   LLQLEQVTRRFGGLVAVNQVSFKVEVGEIFGLIGPNGAGKTTLFNLITGLQPLSGGEICF 62

Query: 69  AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128
            G   +     ++A+ GIARTFQN+RLF +++  ENV+V RH +  + L+  +  +    
Sbjct: 63  QGDRLDRQRPDQIAQRGIARTFQNLRLFNQLSVFENVLVARHRQARTSLWDELIGSSRAT 122

Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188
            +     +R QELL+ + +   AD  A +L+YGD+RRLEIARALA +PQL+ LDEPAAG+
Sbjct: 123 RQSRGDRRRVQELLELLELSDQADQPAASLAYGDRRRLEIARALALEPQLLLLDEPAAGL 182

Query: 189 NATEKVQLRELIDRIRND-NRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKN 247
           N  EK  L + I  IR     T++LIEH V LVMGLCDR+ VLD+G+ IA G+PA V+++
Sbjct: 183 NPREKQDLSDRIRAIREQFQLTVVLIEHHVPLVMGLCDRIAVLDFGQLIALGDPATVRQD 242

Query: 248 EKVIEAYLG 256
             VIEAYLG
Sbjct: 243 PAVIEAYLG 251


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: 218
Number of extensions: 8
Number of successful extensions: 2
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: 253
Length adjustment: 24
Effective length of query: 236
Effective length of database: 229
Effective search space:    54044
Effective search space used:    54044
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: 47 (22.7 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