GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Synechococcus elongatus PCC 7942

Align TreV, component of Trehalose porter (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__SynE:Synpcc7942_1406
          Length = 368

 Score =  188 bits (478), Expect = 2e-52
 Identities = 101/231 (43%), Positives = 153/231 (66%), Gaps = 10/231 (4%)

Query: 18  INGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDK----PPEK 73
           ++ ++ ++E GE   ++GPSG GK+TLL+++AG E L  G I   G  +       PPE 
Sbjct: 24  VDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQRSLPPET 83

Query: 74  RNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKVTQI 133
           R+V MVFQ+YAL+P+++V DN+ F L+ R  K    + R  +A  L+G+  +  +   ++
Sbjct: 84  RSVGMVFQDYALFPHLTVLDNVCFGLRDR--KGSAAVAR--QALALVGLEGLERRYPHEL 139

Query: 134 SGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVTHDQ 193
           SGGQQQRVALARA+   P   LLDEPLSNLD +VR   R EL+ I ++ + T I VTHDQ
Sbjct: 140 SGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQAQATAILVTHDQ 199

Query: 194 KEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLPGE 244
           +EALS+ DR+A++  G+FEQ+  P+ L+++P +++VA+F+ +   NFL  E
Sbjct: 200 EEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLSQ--ANFLATE 248


Lambda     K      H
   0.318    0.137    0.385 

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: 275
Number of extensions: 13
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: 324
Length of database: 368
Length adjustment: 29
Effective length of query: 295
Effective length of database: 339
Effective search space:   100005
Effective search space used:   100005
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.

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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