GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Pontibacter ramchanderi LP43

Align Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized)
to candidate WP_101443030.1 BD749_RS03795 ATP-binding cassette domain-containing protein

Query= SwissProt::P9WQI3
         (393 letters)



>NCBI__GCF_002846395.1:WP_101443030.1
          Length = 259

 Score =  132 bits (331), Expect = 1e-35
 Identities = 73/220 (33%), Positives = 122/220 (55%), Gaps = 13/220 (5%)

Query: 15  DGHTAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGELRIAGERVNEKAPK 74
           D    ++ ++L +  GE L+++G SG GK+  + +I+GL     G + + G  V    P+
Sbjct: 27  DDFEVLKGVDLDLFKGENLVVLGRSGTGKSVLIKIISGLLQADEGSVNVLGREVGALKPR 86

Query: 75  DRD-----IAMVFQSYALYPHMTVRQNIAFPLT-----LAKMRKADIAQKVSETAKILDL 124
           + D     I   FQ+ ALY  MTVR+N+ FPL      + +  + D  Q V E   +L  
Sbjct: 87  ELDALRLKIGFSFQNSALYDSMTVRENLEFPLIRHAKHMTEAEREDTIQYVLEAVGLLQA 146

Query: 125 TNLLDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEIAQLQRRL 184
            N +   PS+LSGGQR+R+ + R ++  P   L DEP + LD    +++   I ++Q + 
Sbjct: 147 INQM---PSELSGGQRKRIGIARTLILKPDIMLYDEPTAGLDPITCIEINSLINEVQEKF 203

Query: 185 GTTTVYVTHDQTEAMTLGDRVVVMYGGIAQQIGTPEELYE 224
            T+++ +THD T A  +GDR+V++  G  Q+ GT +E++E
Sbjct: 204 NTSSIIITHDLTCARAVGDRIVMLLDGQFQREGTFDEVFE 243


Lambda     K      H
   0.319    0.135    0.377 

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: 194
Number of extensions: 11
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: 393
Length of database: 259
Length adjustment: 27
Effective length of query: 366
Effective length of database: 232
Effective search space:    84912
Effective search space used:    84912
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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