GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Sinorhizobium meliloti 1021

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate SM_b20904 SM_b20904 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__Smeli:SM_b20904
          Length = 261

 Score =  190 bits (483), Expect = 2e-53
 Identities = 100/243 (41%), Positives = 161/243 (66%), Gaps = 4/243 (1%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           L+E++++  SFG + A+D  S+++  GEVVALLG NGAGKSTLIKI+SG +K D G+++ 
Sbjct: 8   LVEMKNISISFGGIHAVDDASVDLYPGEVVALLGHNGAGKSTLIKILSGAYKRDAGEILI 67

Query: 64  EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREV-TNKIFLNKKKMMEESK 122
            G+    N+P DA+  GIETIYQ LA+  ++    N++L RE+ T    L+   M  +++
Sbjct: 68  NGEPAEINNPRDAKKYGIETIYQTLAVADNVDAAANLYLGRELRTPWGTLDDVAMEAKAR 127

Query: 123 KLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182
           +++  L          V+ LSGGQRQ+VA+ARA+ F A++++MDEPTAAL   E  +V E
Sbjct: 128 EVMGRLNPNFQRFKEPVKALSGGQRQSVAIARAILFDARILIMDEPTAALGPQETAQVGE 187

Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFAL 242
           L + LK++G+G+ +I+H+I   +++ADR+ V+  G+++ H + E+   +   EV+    +
Sbjct: 188 LIKQLKREGIGIFLISHDIHDVFDLADRVSVMKNGQVVGHARTEDVTKD---EVLGMIIM 244

Query: 243 GKV 245
           GKV
Sbjct: 245 GKV 247


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: 148
Number of extensions: 8
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: 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