GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Snodgrassella alvi wkB2

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_025331514.1 SALWKB2_RS09875 ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_000600005.1:WP_025331514.1
          Length = 311

 Score =  166 bits (419), Expect = 1e-45
 Identities = 87/228 (38%), Positives = 133/228 (58%), Gaps = 1/228 (0%)

Query: 9   LTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMN 68
           + K+F D V   DLSL++ D + + ++G SG GKST L M AGL  P SG+I+I  +++ 
Sbjct: 7   INKKFSDKVVAADLSLEVADGQLVAVLGESGSGKSTLLNMAAGLVQPDSGNIFINEENIT 66

Query: 69  YRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLL 128
           + +P+ R I ++FQDYAL PH+ V QN+ FGL      +  +   + +++   +G+++  
Sbjct: 67  FLLPEQRRIGLMFQDYALLPHLNVWQNVAFGLRMHR-VSKPQAQHQAMQMLAEVGLSEAA 125

Query: 129 DRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTT 188
            R+ D LSGG+QQRVAL RA+V  P+  L+DEP S LD  LRA ++     L  Q     
Sbjct: 126 ARQVDVLSGGEQQRVALARALVLQPQALLLDEPFSALDTTLRASLQQLTVRLLRQQKCPA 185

Query: 189 VYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIG 236
           V VTH+  EA  +ADRI ++  G   Q  +  +    P + + A  +G
Sbjct: 186 VLVTHSPLEAFALADRICLLRHGRWIQQGTAAQLLARPADAWAARLLG 233


Lambda     K      H
   0.317    0.135    0.386 

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: 236
Number of extensions: 9
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: 383
Length of database: 311
Length adjustment: 29
Effective length of query: 354
Effective length of database: 282
Effective search space:    99828
Effective search space used:    99828
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 (21.6 bits)
S2: 49 (23.5 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