GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0027 in Echinicola vietnamensis KMM 6221, DSM 17526

Align TM0027, 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 Echvi_2498 Echvi_2498 Predicted ATPase involved in cell division

Query= TCDB::Q9WXN4
         (268 letters)



>FitnessBrowser__Cola:Echvi_2498
          Length = 232

 Score =  100 bits (248), Expect = 4e-26
 Identities = 69/217 (31%), Positives = 118/217 (54%), Gaps = 23/217 (10%)

Query: 26  VKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRESLV 85
           +++V+F++++ E V L+G +GSGK++  K +   LP   G     G D+ K+IK ++  V
Sbjct: 24  LQDVTFDIEKDEFVFLIGRTGSGKSSLLKTLYADLPLKMGYGKISGYDL-KEIKTKD--V 80

Query: 86  EF-RRKVHAVFQD------PFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLF 138
            F RRK+  VFQD         + N ++ +  T W+          +K +    + E L 
Sbjct: 81  PFLRRKLGIVFQDFQLFTDRTVAENLYFVMRATGWK----------DKAKMKTRMVEVLM 130

Query: 139 RVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLE 198
           RVG+       K PHQ+SGG++QR++IAR  +  P +++ADEPT  +D     GI KL +
Sbjct: 131 RVGLG--GAATKMPHQLSGGEQQRVVIARALLNHPSILLADEPTGNLDPEVADGIFKLFQ 188

Query: 199 ELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVE 235
           E+  +QGT+++  TH+  L       I   + G++++
Sbjct: 189 EI-NKQGTAVLMATHNHDLLNKYPYRILKCEKGKLLD 224


Lambda     K      H
   0.319    0.139    0.397 

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: 167
Number of extensions: 14
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: 268
Length of database: 232
Length adjustment: 24
Effective length of query: 244
Effective length of database: 208
Effective search space:    50752
Effective search space used:    50752
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 (21.7 bits)
S2: 46 (22.3 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