GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Cola:Echvi_2498 Echvi_2498 Predicted ATPase
           involved in cell division
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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