GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Desulfoscipio geothermicus DSM 3669

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_092482139.1 BM299_RS03860 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_900115975.1:WP_092482139.1
          Length = 390

 Score =  168 bits (425), Expect = 3e-46
 Identities = 90/228 (39%), Positives = 135/228 (59%), Gaps = 7/228 (3%)

Query: 14  GDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDH-MNYRVP 72
           G TV + + S  +++ E  V++G SG GKST +R L  L  PT+G+IY+ GD+ + Y   
Sbjct: 39  GHTVGIRNASFQVEEGEVFVIMGLSGSGKSTLIRCLNLLNKPTAGEIYVDGDNILEYDKK 98

Query: 73  Q-----NRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADL 127
           Q        +AMVFQ + L  H TV  N+ +GLE ++     ER E   +     G+A  
Sbjct: 99  QLKKFRQEKVAMVFQHFGLLSHRTVIGNVEYGLEVKK-IPKNERCEIAKKAIANAGLAGW 157

Query: 128 LDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVT 187
            ++ P+ELSGG QQRV L RA+  DP++ LMDEP S LD  +R +M+ EL  LQ +L  T
Sbjct: 158 ENKMPNELSGGMQQRVGLARALANDPDILLMDEPFSALDPLIRRDMQYELMELQSRLKKT 217

Query: 188 TVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFI 235
            +++TH+  EA  + DR+AVM DG ++Q+ +P E    P + ++  F+
Sbjct: 218 IIFITHDINEAFKIGDRVAVMKDGVIEQIGTPEELLASPESEYIENFV 265


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: 291
Number of extensions: 12
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: 390
Length adjustment: 30
Effective length of query: 353
Effective length of database: 360
Effective search space:   127080
Effective search space used:   127080
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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