GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pedobacter sp. GW460-11-11-14-LB5

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein

Query= uniprot:A0A165KQ08
         (355 letters)



>FitnessBrowser__Pedo557:CA265_RS07485
          Length = 252

 Score =  137 bits (345), Expect = 3e-37
 Identities = 76/220 (34%), Positives = 122/220 (55%), Gaps = 8/220 (3%)

Query: 5   LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64
           + I  I +++  G + +  L+ V + +  GEF+ L+GPSG GKSTL+NI+  LD P+ G 
Sbjct: 6   ITIKEIGRKYVIGSEVIHALKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGT 65

Query: 65  IRIGGKNVVGMPP------RDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKR 118
             + G NV  M        R+++I  VFQ++ L P  +  DN+   L      K +R  R
Sbjct: 66  YVLNGTNVSHMSDDALAEVRNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGTSKKDRDAR 125

Query: 119 IDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMR 178
                  + + + +D +P++LSGGQRQRVA+ RAL   P + L DEP  NLD K  +E+ 
Sbjct: 126 AARALENVGLGNRMDHKPNELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIM 185

Query: 179 AEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQ 218
             ++ +H + G T + VTH++ +      RI  M+ G+++
Sbjct: 186 GLLEEIH-SKGNTIILVTHEE-DIAQHAHRIVRMRDGLIE 223


Lambda     K      H
   0.318    0.135    0.388 

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: 10
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: 355
Length of database: 252
Length adjustment: 27
Effective length of query: 328
Effective length of database: 225
Effective search space:    73800
Effective search space used:    73800
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 (21.7 bits)
S2: 48 (23.1 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