GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Sphingomonas koreensis DSMZ 15582

Align BadI (characterized)
to candidate Ga0059261_2668 Ga0059261_2668 Enoyl-CoA hydratase/carnithine racemase

Query= metacyc::MONOMER-892
         (260 letters)



>FitnessBrowser__Korea:Ga0059261_2668
          Length = 256

 Score =  108 bits (270), Expect = 1e-28
 Identities = 82/260 (31%), Positives = 121/260 (46%), Gaps = 13/260 (5%)

Query: 4   EDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFC 63
           +DL++ + + VA I +NRP K+NA        LI ++        V  +V+ GAG++AF 
Sbjct: 3   DDLLFTVADHVATITLNRPAKLNALTPEMAAALIASVSACNSSDAVRCVVITGAGEKAFS 62

Query: 64  TGGDQSTHDGN---YDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICDL 120
            G D +T DG    +D R       ++   A+R   KPV+A + GYA+GGG   A   D+
Sbjct: 63  AGSDITTLDGYATPWDFRNR-----DDYCDALRACRKPVVAAINGYALGGGLETAMAADI 117

Query: 121 TICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANL 180
            I S  A F     K+G +  G   A L   +G   A  + +       ++A A GL + 
Sbjct: 118 RIASTNARFAAPEIKLGWIGGGGMAAGLTYSMGASNAALMLFTGDMIDAEKALAWGLVSE 177

Query: 181 CVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKLY---YDT 237
            V  D L A  Q+    +  R+P A   AK   N+  AH         Y   L    + T
Sbjct: 178 VVAPDALLARAQEIARTIASRAPIAAETAK--LNLRAAHTMPWDKAIEYERDLQAICFAT 235

Query: 238 DESREGVKALQEKRKPEFRK 257
           D+++EG  A  EKR P FR+
Sbjct: 236 DDAKEGRAAFAEKRAPVFRR 255


Lambda     K      H
   0.319    0.138    0.418 

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: 176
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: 260
Length of database: 256
Length adjustment: 24
Effective length of query: 236
Effective length of database: 232
Effective search space:    54752
Effective search space used:    54752
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: 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