GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Rhizorhabdus wittichii RW1

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  128 bits (322), Expect = 2e-34
 Identities = 77/224 (34%), Positives = 118/224 (52%), Gaps = 4/224 (1%)

Query: 4   IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63
           I    + K +     +DD+SL I+   F+ LVG SG GK+T L+ +  L    +G I I 
Sbjct: 2   ISFDHVGKHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIE 61

Query: 64  GDHMNYR--VPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAET 121
           G  +  +      R I  VFQ   L+PHM+V +N+   +   +G    ER  RV E+ + 
Sbjct: 62  GRDVAAQPVAELRRRIGYVFQGIGLFPHMSVAENVAL-VPRLQGVPREERAARVAELLDL 120

Query: 122 LGI-ADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180
           + + AD  +R+P +LSGGQ QRV   RA+   P + LMDEP   LD   R E+    + L
Sbjct: 121 VALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRAL 180

Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYH 224
            + + +T++ VTH+  EA+ +ADR+ V+ +G +     P    H
Sbjct: 181 HEAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALIH 224


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: 196
Number of extensions: 6
Number of successful extensions: 3
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: 252
Length adjustment: 27
Effective length of query: 356
Effective length of database: 225
Effective search space:    80100
Effective search space used:    80100
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: 48 (23.1 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