GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacK in Dinoroseobacter shibae DFL-12

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 3607842 Dshi_1250 ABC transporter related (RefSeq)

Query= uniprot:D4GP39
         (383 letters)



>lcl|FitnessBrowser__Dino:3607842 Dshi_1250 ABC transporter related
           (RefSeq)
          Length = 351

 Score =  297 bits (760), Expect = 3e-85
 Identities = 165/368 (44%), Positives = 225/368 (61%), Gaps = 19/368 (5%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           M+ +TL    K Y     G+   V  + L I DGEF V VGPSGCGKST LRM+AGLE  
Sbjct: 1   MSGITLRGAVKRY-----GETQVVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEET 55

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
           +EG + +  R +  +   +R +AMVFQ+YALYPH +V  NM FGL+ + G+P  EI+ +V
Sbjct: 56  SEGSIHIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMN-GVPKAEIKAKV 114

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
              +++L + D L RKP  LSGGQ+QRVA+GRAIVR PEVFL DEPLSNLDA+LR EMR 
Sbjct: 115 AAASEILKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRV 174

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           E+ RL  E+G T +YVTHDQ EAMT+ D++ VL  G ++QVG PL+ Y  P+N+FVAGFI
Sbjct: 175 EIARLHKEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFI 234

Query: 241 GEPSMNLFDGSLSGDTFRGDGF-DYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQR 299
           G P+MN  DG +  D     G    P+ GA     G +  +T+G+RP+ + +     G  
Sbjct: 235 GSPAMNFLDGRIENDAVHLAGLPPLPVPGAA----GRSGPVTVGVRPQHIALEPGGDGYL 290

Query: 300 TFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFD 359
                V + E  G  + ++LR   G +G++ T     +  +  G    +S   D + LF+
Sbjct: 291 -----VELTESLGGVSYLYLR---GADGSRLTVEAGEEDPIAEGTPVGLSLAPDRVMLFE 342

Query: 360 GETGDALK 367
            ETG  L+
Sbjct: 343 AETGQRLR 350


Lambda     K      H
   0.316    0.136    0.384 

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: 441
Number of extensions: 27
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: 351
Length adjustment: 30
Effective length of query: 353
Effective length of database: 321
Effective search space:   113313
Effective search space used:   113313
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: 42 (22.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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