GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0028 in Dyella japonica UNC79MFTsu3.2

Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate N515DRAFT_1821 N515DRAFT_1821 putative ABC transport system ATP-binding protein

Query= TCDB::Q9WXN5
         (330 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1821
          Length = 238

 Score = 88.2 bits (217), Expect = 2e-22
 Identities = 74/238 (31%), Positives = 118/238 (49%), Gaps = 17/238 (7%)

Query: 5   LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPL- 63
           +LK  ++   Y+ E V   A+   + ++ E E + V G SG GKTT     F+ +   L 
Sbjct: 1   MLKMTHLSKVYRTEVVETYALRDFNIDVKEGEFVAVTGPSGSGKTT-----FLTIAGLLE 55

Query: 64  TLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLA 123
           T   G+  L    + VE+S++  D  + K   ++I  I QA    L+P + +   V    
Sbjct: 56  TFTGGEYHL----DGVEVSNLN-DNARSKIRNEKIGFIFQAFN--LIPDLNVYDNVEVPL 108

Query: 124 ESHGIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADE 183
              G+   E   +     E VGL     K YP ELSGG +QR  IA A   +P LL+ADE
Sbjct: 109 RYRGMKALERKQRIMDALERVGLASR-AKHYPAELSGGQQQRVAIARALAGSPRLLLADE 167

Query: 184 PTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFA 241
           PT  LD    + ++++L ++ R+G   +I+ +THD     + A R + +  G++V+ A
Sbjct: 168 PTGNLDTQMARGVMELLEEIHREG--ATIVMVTHDPELATR-AQRNVHVIDGQVVDLA 222


Lambda     K      H
   0.321    0.138    0.405 

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: 150
Number of extensions: 7
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: 330
Length of database: 238
Length adjustment: 26
Effective length of query: 304
Effective length of database: 212
Effective search space:    64448
Effective search space used:    64448
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: 47 (22.7 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