GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Rhizobium freirei PRF 81

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_037150766.1 RHSP_RS09200 sugar ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>NCBI__GCF_000359745.1:WP_037150766.1
          Length = 273

 Score =  197 bits (502), Expect = 1e-55
 Identities = 105/237 (44%), Positives = 159/237 (67%), Gaps = 6/237 (2%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           +L ++ + K FGAV AL  ++++++ GEVVAL+GDNGAGKSTL+K+++G H+P  G + F
Sbjct: 15  VLSLKGISKHFGAVSALTDINLDVHAGEVVALVGDNGAGKSTLVKVLAGVHQPSSGTITF 74

Query: 64  EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123
            GK+V  + P  A  LGI T++QDLAL  +L +  NIFL RE+ + I L++  M   +  
Sbjct: 75  RGKQVTLSDPATALDLGIATVFQDLALCENLDVVANIFLGREL-SPIKLDETAMEVRAWT 133

Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183
           LL+ L  RIP + + + +LSGGQRQ VA+AR++    K+I++DEPTAAL V +  +VL L
Sbjct: 134 LLNELAARIPSVRIPIASLSGGQRQTVAIARSLLLEPKLIMLDEPTAALGVAQTAEVLNL 193

Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKI--IFHKKKEETNVEEITEVMT 238
              ++ KGLGV++I+HN+     VADRI VL  G+   IF+    +T+ +E+   +T
Sbjct: 194 IERVRDKGLGVIMISHNMEDVRAVADRIVVLRLGRNNGIFY---PDTSNQELVSAIT 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: 162
Number of extensions: 7
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: 273
Length adjustment: 25
Effective length of query: 226
Effective length of database: 248
Effective search space:    56048
Effective search space used:    56048
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 24 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