GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0930 N515DRAFT_0930
           methylglutaconyl-CoA hydratase
          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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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