GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Synechococcus elongatus PCC 7942

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase

Query= uniprot:Q6MNM2
         (347 letters)



>FitnessBrowser__SynE:Synpcc7942_1406
          Length = 368

 Score =  194 bits (494), Expect = 2e-54
 Identities = 103/225 (45%), Positives = 150/225 (66%), Gaps = 10/225 (4%)

Query: 22  IDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGKKI----NDIEPQNRDI 77
           +  ++  GE L LVGPSGCGK+TLLR +AG ES  SG+I + G+ +      + P+ R +
Sbjct: 27  VSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQRSLPPETRSV 86

Query: 78  AMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQIKHLLDRKPKELSGG 137
            MVFQ YAL+PH+TV +N+ FGL+ +  +AA   + +     L+ ++ L  R P ELSGG
Sbjct: 87  GMVFQDYALFPHLTVLDNVCFGLRDRKGSAAVARQAL----ALVGLEGLERRYPHELSGG 142

Query: 138 QRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKSTMIYVTHDQMEA 197
           Q+QRVAL RAL+ Q P+IL DEPLSNLD  +R ++R E++ +   +++T I VTHDQ EA
Sbjct: 143 QQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQAQATAILVTHDQEEA 202

Query: 198 TTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFL 242
            ++ DR+AV++ G  EQIG P E++  P + F+A F+   + NFL
Sbjct: 203 LSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLS--QANFL 245


Lambda     K      H
   0.318    0.136    0.383 

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: 267
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: 347
Length of database: 368
Length adjustment: 29
Effective length of query: 318
Effective length of database: 339
Effective search space:   107802
Effective search space used:   107802
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