GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Tistlia consotensis USBA 355

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085126658.1 B9O00_RS29715 ATP-binding cassette domain-containing protein

Query= uniprot:P0DTT6
         (251 letters)



>NCBI__GCF_900177295.1:WP_085126658.1
          Length = 260

 Score =  200 bits (508), Expect = 3e-56
 Identities = 104/231 (45%), Positives = 157/231 (67%), Gaps = 1/231 (0%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           L+E+R +  +FG VKA+DGVS+++  GEVV LLG NGAGKSTLIK++SG      G+++ 
Sbjct: 8   LVEMRGIEVAFGGVKAVDGVSLDLYAGEVVGLLGHNGAGKSTLIKVLSGAVPARAGEILI 67

Query: 64  EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI-FLNKKKMMEESK 122
           +G  V   SP DAR   IETIYQ LAL  +L    N+FL RE+T     L++++M  E++
Sbjct: 68  DGAAVRIASPQDARRHRIETIYQTLALADNLNAAANLFLGRELTTPTGLLDEERMEAETR 127

Query: 123 KLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182
           ++L  L       +  V +LSGGQRQ++A+ARAV+F A++++MDEPTAAL V E   V E
Sbjct: 128 RILARLNRNFDRFSTPVRSLSGGQRQSIAIARAVHFDARILIMDEPTAALGVQETAMVAE 187

Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEI 233
           L R LK +G+G+ +I+H+I   ++++DR+ VL  G+++  ++  ET  +E+
Sbjct: 188 LVRQLKAEGIGIFLISHDIHDVFDLSDRVTVLKNGRLVGTRRVAETTQDEV 238


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: 138
Number of extensions: 5
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: 260
Length adjustment: 24
Effective length of query: 227
Effective length of database: 236
Effective search space:    53572
Effective search space used:    53572
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 Apr 09 2024. 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