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_025331193.1 SALWKB2_RS08205 polyamine ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_000600005.1:WP_025331193.1
          Length = 376

 Score =  235 bits (599), Expect = 2e-66
 Identities = 130/303 (42%), Positives = 181/303 (59%), Gaps = 28/303 (9%)

Query: 4   IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63
           +Q+ D+ K +GD  AVD ++L I   E   L+G SG GKST LRMLAG+ETPT G I + 
Sbjct: 17  LQIKDIVKTYGDNYAVDHINLTIKKNEIFALLGSSGSGKSTLLRMLAGMETPTQGQIILD 76

Query: 64  GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123
           G+ +    P +R I M+FQ YAL+PHMTV QNI FGL++++     E   RV E+   + 
Sbjct: 77  GEDITKLQPYDRPINMMFQSYALFPHMTVEQNIAFGLKQDK-LPKDEISARVEEMLRLVQ 135

Query: 124 IADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQ 183
           ++    RKP +LSGGQQQRVAL R++ + P++ L+DEPL  LD KLR + + EL N  ++
Sbjct: 136 MSKYAKRKPHQLSGGQQQRVALARSLAKRPKLLLLDEPLGALDKKLRQQTQLELVNTLEK 195

Query: 184 LAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINLV 243
           +  T + VTH+Q EAMTMA RIA+M DG+LQQV +P + Y  PN+ F AEF+GE   N++
Sbjct: 196 VGATCIMVTHDQEEAMTMASRIAIMSDGQLQQVGTPSDIYDYPNSRFTAEFMGE--TNIL 253

Query: 244 RGTRSES---------------TFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVAD 288
            G  +E                 ++G   S P D+ +           L +RPEDI +  
Sbjct: 254 EGKVTEDGADHTIIHCPEMQQLVYLGHGISGPEDQKIW----------LSIRPEDINIYR 303

Query: 289 AAP 291
             P
Sbjct: 304 EQP 306


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: 332
Number of extensions: 14
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: 376
Length adjustment: 30
Effective length of query: 353
Effective length of database: 346
Effective search space:   122138
Effective search space used:   122138
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: 50 (23.9 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