GapMind for catabolism of small carbon sources

 

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

Align BadK (characterized)
to candidate N515DRAFT_0930 N515DRAFT_0930 methylglutaconyl-CoA hydratase

Query= metacyc::MONOMER-943
         (258 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0930
          Length = 264

 Score =  120 bits (301), Expect = 3e-32
 Identities = 92/253 (36%), Positives = 136/253 (53%), Gaps = 14/253 (5%)

Query: 14  VGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADI---ASM 70
           V  +T+NRP V NA +D+L+  L  AL A   D+ + A+V+ G   +F+AGAD+     M
Sbjct: 13  VRTVTMNRPQVHNAFDDSLIAELTDALAAAGRDENVRAVVLTGAGASFSAGADLNWMRGM 72

Query: 71  AAWSYSDVYGSNF-ITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFA 129
           A  S ++    +  +     T++ + KP +A V G AYGGG  L   CDI I   SAKF 
Sbjct: 73  AKASEAENREDSLRLAALMRTLQFLPKPTVARVNGAAYGGGVGLIACCDIAIGVDSAKFG 132

Query: 130 LPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDE 189
           L E+KLGL+P A  +  +  AIG  ++  + L+    +A  A R GL+ + V  + L D 
Sbjct: 133 LTEVKLGLVP-AVISPYVIAAIGLRQSRRLFLTGELFDASTAQRIGLLHQCVRAEELDD- 190

Query: 190 TVALATTIAAFSAPALMALKESLNRAF-----ESTLAEGILFERRELHARF-ASADAREG 243
             ALA  +AAF+    +A  ++   A      +   AE I  E  EL AR   SA+ +EG
Sbjct: 191 --ALAGVLAAFAKAGPVAQAQAKRLALRVAGQDQAQAERIDRENAELIARLRVSAEGQEG 248

Query: 244 IQAFLEKRAPCFS 256
           + AFL+KRA  ++
Sbjct: 249 LGAFLDKRAAAWT 261


Lambda     K      H
   0.321    0.135    0.389 

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: 120
Number of extensions: 7
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: 258
Length of database: 264
Length adjustment: 25
Effective length of query: 233
Effective length of database: 239
Effective search space:    55687
Effective search space used:    55687
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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