GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pontibacter ramchanderi LP43

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_101443030.1 BD749_RS03795 ATP-binding cassette domain-containing protein

Query= uniprot:A0A165KQ08
         (355 letters)



>NCBI__GCF_002846395.1:WP_101443030.1
          Length = 259

 Score =  140 bits (352), Expect = 5e-38
 Identities = 79/230 (34%), Positives = 131/230 (56%), Gaps = 11/230 (4%)

Query: 5   LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64
           + I G+ K F       EVL+ VD+ +  GE L+++G SG GKS L+ II+GL +  EG 
Sbjct: 17  ISIRGLKKAFD----DFEVLKGVDLDLFKGENLVVLGRSGTGKSVLIKIISGLLQADEGS 72

Query: 65  IRIGGKNVVGMPPRDRD-----IAMVFQSYALYPTLSVADNIGFAL--EMRKMPKPERQK 117
           + + G+ V  + PR+ D     I   FQ+ ALY +++V +N+ F L    + M + ER+ 
Sbjct: 73  VNVLGREVGALKPRELDALRLKIGFSFQNSALYDSMTVRENLEFPLIRHAKHMTEAERED 132

Query: 118 RIDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEM 177
            I  V   + +   +++ PS+LSGGQR+R+ + R L  +P + L+DEP + LD    +E+
Sbjct: 133 TIQYVLEAVGLLQAINQMPSELSGGQRKRIGIARTLILKPDIMLYDEPTAGLDPITCIEI 192

Query: 178 RAEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIY 227
            + I  + +    +S+ +THD   A  +G RI ++  G  Q+ GT DE++
Sbjct: 193 NSLINEVQEKFNTSSIIITHDLTCARAVGDRIVMLLDGQFQREGTFDEVF 242


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: 180
Number of extensions: 8
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: 355
Length of database: 259
Length adjustment: 27
Effective length of query: 328
Effective length of database: 232
Effective search space:    76096
Effective search space used:    76096
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 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