GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Synechococcus elongatus PCC 7942

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate Synpcc7942_0249 Synpcc7942_0249 ATPase

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__SynE:Synpcc7942_0249
          Length = 261

 Score =  110 bits (275), Expect = 3e-29
 Identities = 68/217 (31%), Positives = 124/217 (57%), Gaps = 13/217 (5%)

Query: 10  VHKSFG-AVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKV 68
           V K +G   +AL GVS+ + +GEVV ++G +G+GKST ++ ++      RG++  EG ++
Sbjct: 27  VEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRL 86

Query: 69  IFNSPNDARSLG-----IETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123
                +D R +      +  ++Q   L P L +  N+ LA     +  + + +    +++
Sbjct: 87  ----SHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEAT--ARQ 140

Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183
           LL+ ++I     +     LSGGQ+Q VA+ARA+    +++L DEPT+AL     R+VL++
Sbjct: 141 LLERVRIA-EQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDV 199

Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220
            R+L  +G+ +L+ TH +    EVADR+ ++  G+I+
Sbjct: 200 MRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIV 236


Lambda     K      H
   0.318    0.137    0.371 

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: 102
Number of extensions: 3
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: 251
Length of database: 261
Length adjustment: 24
Effective length of query: 227
Effective length of database: 237
Effective search space:    53799
Effective search space used:    53799
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: 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