GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Sinorhizobium meliloti 1021

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate SMc01980 SMc01980 sugar transport system ATP-binding ABC transporter protein

Query= uniprot:D4GP38
         (383 letters)



>FitnessBrowser__Smeli:SMc01980
          Length = 355

 Score =  286 bits (731), Expect = 8e-82
 Identities = 165/367 (44%), Positives = 215/367 (58%), Gaps = 21/367 (5%)

Query: 1   MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60
           M  I + ++ K +G    + D+ L I D EF+VLVGPSGCGKST LRM+AGLE+ T G+I
Sbjct: 1   MASIDIANIKKSYGTHPVLHDVDLKISDGEFVVLVGPSGCGKSTLLRMIAGLESVTGGEI 60

Query: 61  YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVE-VA 119
            I G  +N   P++RDIAMVFQ YALYPHM+V +N+ + L   +  T+ +R   VV   A
Sbjct: 61  RIAGRRVNELAPKDRDIAMVFQSYALYPHMSVARNMSYSLRLRK--TAKDRITTVVAGAA 118

Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179
             LG+  LLDR+P  LSGGQ+QRVA+GRAIVR P+ FL DEPLSNLDA+LR +MR E++ 
Sbjct: 119 AKLGLDPLLDRRPKALSGGQRQRVAMGRAIVRQPKAFLFDEPLSNLDARLREQMRAEIKK 178

Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239
           L   L  T++YVTH+Q EAMT+ADRI  M+ G +QQV SP + Y  P NLFVA FIG P 
Sbjct: 179 LHKDLGATSIYVTHDQIEAMTLADRIVAMNGGVVQQVGSPLDLYDRPANLFVAGFIGSPG 238

Query: 240 INLVRGTRSESTF----VGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAA 295
           +N   G           + +    PL  D    V +     LG+RPE + +A   P+   
Sbjct: 239 MNFFEGAYHAGDAPRFEMSDEIGIPL--DAAAPVSNNSKVTLGIRPEHVVLAGHGPE--- 293

Query: 296 LDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDK 355
                L   V +VEP G   +LHLS         A +  T     +T    + V  P   
Sbjct: 294 ----TLLAGVDLVEPTGFGIILHLS-----LGRAAFKVFTNDRSFLTASGTIPVHFPAHH 344

Query: 356 IHLFDAE 362
           +H FDAE
Sbjct: 345 LHFFDAE 351


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: 340
Number of extensions: 13
Number of successful extensions: 4
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: 355
Length adjustment: 30
Effective length of query: 353
Effective length of database: 325
Effective search space:   114725
Effective search space used:   114725
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 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