GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Dethiosulfovibrio salsuginis USBA 82

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085544626.1 B9Y55_RS06870 ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_900177735.1:WP_085544626.1
          Length = 363

 Score =  221 bits (564), Expect = 2e-62
 Identities = 108/223 (48%), Positives = 152/223 (68%), Gaps = 1/223 (0%)

Query: 15  DTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMNYRVPQN 74
           +  AV D    I+  E + L+GPSGCGK+TTLRM+ G E PT G I+IG D + Y  P  
Sbjct: 25  NVTAVKDSDFVIEPGELVTLLGPSGCGKTTTLRMIGGFEVPTRGRIFIGSDDVTYLPPNQ 84

Query: 75  RDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRKPDE 134
           RD AMVFQ Y L+PHM V  N+ +GL+  +   S + +++V E    +G+ +L  R P  
Sbjct: 85  RDTAMVFQSYGLFPHMNVFDNVAYGLKLRK-VPSQDIEKKVTEFLRMVGLEELAKRPPSR 143

Query: 135 LSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYVTHN 194
           LSGGQQQRVAL R+++ +P V L+DEPLSNLDA LR +MR E++ +Q  L +T VYVTH+
Sbjct: 144 LSGGQQQRVALARSLIVEPGVLLLDEPLSNLDALLREQMRVEIRRIQKSLNITAVYVTHD 203

Query: 195 QTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGE 237
           + EAM+++DR+ VMD GE+ Q+ +P + Y +P + FVA F+G+
Sbjct: 204 RVEAMSLSDRVIVMDRGEVVQIGTPSQIYCDPVSSFVAGFVGK 246


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: 335
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: 363
Length adjustment: 30
Effective length of query: 353
Effective length of database: 333
Effective search space:   117549
Effective search space used:   117549
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